Mycobacteriophages ElvisPhasley and Mesmerelda were isolated from soil and infect Mycobacterium smegmatis. Each phage has siphovirus morphology and encodes 102 genes. Based on broader genomic similarity to actinobacteriophages, both are assigned to the B1 subcluster.
","acknowledgements":"We thank the University of Pittsburgh for genome sequencing, Old Dominion University Applied Research Center for the TEM images, the Hatfull lab, and the entire SEA-PHAGES program for their considerable ongoing support. We also thank the many institutions with SEA-PHAGES programs for their discovery and annotation of phages which made the Gepard plot in Figure 1f possible.
","authors":[{"affiliations":["William and Mary"],"departments":[""],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"vafiggins@wm.edu","firstName":"Victoria","lastName":"Figgins","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"gehussey@wm.edu","firstName":"Grace","lastName":"Hussey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["dataCuration","formalAnalysis","investigation","validation","writing_originalDraft","writing_reviewEditing"],"email":"shaimowitz@wm.edu","firstName":"Sarah","lastName":"Haimowitz","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"vpande@wm.edu","firstName":"Vera","lastName":"Pande","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"moroyster@wm.edu","firstName":"Marcus","lastName":"Royster","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egflanagan@wm.edu","firstName":"Emmery","lastName":"Flanagan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"mefountain@wm.edu","firstName":"Me'Shar'li'a","lastName":"Fountain","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egeorge@wm.edu","firstName":"Erin","lastName":"George","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zmherring@wm.edu","firstName":"Zion","lastName":"Herring","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"smjensen@wm.edu","firstName":"Scarlett","lastName":"Jensen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"jnnguyen@wm.edu","firstName":"Jenny","lastName":"Nguyen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"klonufer@wm.edu","firstName":"Konur","lastName":"Onufer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"plsmith02@wm.edu","firstName":"Phoenix","lastName":"Smith","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"bfstrong@wm.edu","firstName":"Brennan","lastName":"Strong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zwang64@wm.edu","firstName":"Bruce","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"ayang02@wm.edu","firstName":"Abigail","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":[""],"credit":["formalAnalysis","validation","writing_reviewEditing","visualization"],"email":"hlqian@wm.edu","firstName":"Heather","lastName":"Qian","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Biology Department and Applied Science Department"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","project","resources","supervision","validation","visualization","writing_originalDraft","writing_reviewEditing","fundingAcquisition"],"email":"mssaha@wm.edu","firstName":"Margaret","lastName":"Saha","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-0096-2667"}],"awards":[{"awardId":"1R15HD096415-01 ","funderName":"National Institutes of Health (United States)","awardRecipient":"Margaret Saha"}],"conflictsOfInterest":null,"dataTable":null,"extendedData":[],"funding":"","image":{"url":"https://portal.micropublication.org/uploads/86c99ad108dbcdb759e8377b03726a3e.png"},"imageCaption":"Plaque image of ElvisPhasley (a) showing clear plaques with translucent halos. and of Mesmerelda (b) showing clear plaques. Scale bars for plaque images are 12.5 mm. Negative stain (uranyl acetate, 1%) transmission electron microscopy (TEM) of ElvisPhasley (c) and Mesmerelda (d) revealing siphoviral morphology. Scale bar for micrographs are 50 nm. (e) Gepard plot comparing the genomic sequences of 40 B1 cluster phages, including ElvisPhasley and Mesmerelda, and 10 B2 cluster phages. Both axes represent all 50 phage gnomes, and each line of the dot plot represents a phage. The Gepard plot exemplifies the genomic similarities of ElvisPhasley and Mesmerelda to other B1 cluster phages and the genomic dissimilarity of ElvisPhasley and Mesmerelda to B2 cluster phages. (f) Alignment of ElvisPhasley and Mesmerelda using Phamerator. The genome is represented by the ruler, in kilo base pairs, with boxes above and below the ruler representing forward and reverse transcribed genes, respectively, and gene numbers presented within the box.
","imageTitle":"Plaque and TEM Images and Genomic Organization of ElvisPhasely and Mesmerelda
","methods":"","reagents":"","patternDescription":"Advancing the characterization of mycobacteriophages, bacteriophages that infect Mycobacterium hosts, is of interest due to increasing antibiotic resistance in pathogenic Mycobacterium species (Hatfull, 2020; Hatfull, 2022; Bonacorsi et al., 2024). Mycobacteriophage engineering is a promising approach in the detection and treatment of mycobacterial infections (Bonacorsi et al., 2024; Hosseiniporgham et al., 2022). Therefore, the continued characterization of mycobacteriophages broadens the capabilities of bioengineers in combating this global issue. Here, we report the genome sequences of two novel mycobacteriophages, ElvisPhasley and Mesmerelda.
Phages were isolated from two different soil samples: ElvisPhasley from wet, silty soil on the William & Mary campus in Williamsburg, VA; Mesmerelda from a bag of commercially available garden soil (Table 1). A standard enrichment procedure was followed for both samples: 5 g of each sample was suspended in 45 mL of 7H9 media, inoculated with Mycobacterium smegmatic mc2 155, and incubated in a 37°C shaker at 250 rpm for 48 hours (Zorawik et al., 2024). Rsultant cultures were filtered using a 0.22 µm filter, and filtrates were plated in 7H9 top agar with M. smegmatis. After 24-48 hours, both ElvisPhasley and Mesmerelda produced clear plaques (Fig. 1a-b). Both phages were purified with three rounds of plating, and a high titer lysate was prepared by flooding webbed plates with phage buffer (10 mM Tris, pH 7.5; 10 mM MgSO4; 68 mM NaCl; 1 mM CaCl2). Negative stain (1% uranyl acetate) transmission electron microscopy of each lysate revealed siphovirus morphology for both phages (Fig. 1c-d).
Phage DNA was extracted from each high titer lysate using a phenol-chloroform-isoamyl alcohol procedure and ethanol precipitation (Sambrook and Russell, 2006). DNA was prepared for sequencing using the NEB Ultra II Library Kit and sequenced using an Illumina NextSeq 1000 sequencer (single-end, 100 base read). Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) (Martin, 2011; Jiang et al., 2014; Wick et al., 2017). Newbler (v.2.9) was then used to assemble the genome and Consed (v.29) to check for completeness (Russell, 2018; Gordon et al., 1998). Sequencing data and genome characteristics are presented in Table 1.
Genome annotation was performed using DNA Master (v.5.23.6) and PECAAN (v.20221109) (Rinehart et al., 2016; Pope and Jacobs-Sera, 2018). Open reading frames (ORFs) were predicted using Glimmer (v.3.02) and GeneMark (v.2.5) (Besemer and Borodovsky, 2005; Delcher et al., 2007), coding potential was verified using GeneMark (Besemer and Borodovsky, 2005), and start site similarity in homologs was found using BLASTp and Starterator (http://phages.wustl.edu/starterator/) against the NCBI non-redundant protein and Actinobacteriophage databases (Altschul et al., 1990). No tRNAs were predicted using Aragorn (v.1.2.41) and tRNAscan (Laslett and Canback, 2004; Lowe and Eddy, 1997).
Predictions from HHPred (using the PDB_mmCIF70, NCBI_CD, SCOPe70, and pFAM-A databases), BLASTp, and Phamerator for highly similar genes were used to assign putative gene functions (Cresawn et al., 2011; Zimmermann et al., 2018). Both phages are assigned to cluster B, subcluster B1 using the gene content similarity (GCS) tool at the Actinobacteriophage database, PhagesDB, and clustering parameters of at least 35% GCS to actinobacteriophages (Russell and Hatfull, 2017). Default settings were used for all software.
The genomes of ElvisPhasley and Mesmerelda both encode 102 protein-coding genes, with 33 and 32 genes, respectively, assigned functions involved in virion propagation, structure, and lysis. As neither ElvisPhasley nor Mesmerelda encode a putative integrase or other proteins implicated in lysogeny, these phages are predicted to be virulent. Both ElvisPhasley and Mesmerelda display strong genomic similarity to other B1 subcluster phages and genomic dissimilarity to B2 subcluster phages as displayed on a Gepard dot plot (Fig. 1f; Krumsiek et al., 2007). ElvisPhasley shares 89.22% GCS with its closest relative, OSMaximus (Russell and Hatfull, 2017). At the nucleotide level, ElvisPhasley shares 99.00% identity with OSMaximus over 97% coverage (BLAST). Within this covered region, we identified 968 nucleotide differences, 249 of which were found in coding regions. Of these differences, 238 resulted in amino acid substitutions, 98 of which were conservative and 140 of which were non-conservative as classified by the BLOSUM62 alignment score matrix. Likewise, Mesmerelda shares 95.1% GCS with its closest relative, Orfeu (Russell and Hatfull, 2017). These phages share 99.16% nucleotide identity over 100% coverage. Of the 557 nucleotide differences, 136 differences occur in coding regions. These differences result in 115 amino acid substitutions, 53 of which are conservative and 62 of which are not conservative.
Nucleotide sequence accession numbers
ElvisPhasley and Mesmerelda are available at GenBank with Accession No. PV876949 and PV876954, and Sequence Read Archive (SRA) No. SRX29990110 and SRX29990101.
Table 1: Genome and sequencing information for Mesmerelda and ElvisPhasley
Phage | ElvisPhasley | Mesmerelda |
Isolation GPS Coordinates | 37° 16' 13.4034\" N 76° 43' 3.216\" W | 37° 16' 11.8992\" N 76° 42' 52.5996\" W |
Morphology | Siphovirus | Siphovirus |
Capsid diameter | 60 ± 4 nm (n = 5) | 50 ± 4 nm (n = 5) |
Tail length | ~310 ± 10 nm (n = 5) | ~220 ± 10 nm (n = 5) |
Sequencing reads | 4,697,092 | 4,305,175 |
Sequencing coverage, fold | 6,513 | 5,969 |
Genome length (bp) | 69,502 | 68,890 |
Character of genome ends | Circularly permuted | Circularly permuted |
Number of protein-coding genes | 102 | 102 |
GC content (%) | 66.4 | 66.4 |
Accession number | PV876949 | PV876954 |
SRA | SRX29990110 | SRX29990101 |
Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Bonacorsi A, Ferretti C, Di Luca M, Rindi L. 2024. Mycobacteriophages and Their Applications. Antibiotics. 13: 926.","pubmedId":"","doi":"10.3390/antibiotics13100926"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. Cresawn2011.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, dynamics, and applications. Annu. Rev. Virol. 7: 37-61.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF. 2022. Mycobacteriophages: From Petri dish to patient. PLoS Pathog. 18: e1010602.","pubmedId":"","doi":"10.1371/journal.ppat.1010602"},{"reference":"Hosseiniporgham S, Sechi LA. 2022. A Review on Mycobacteriophages: From Classification to Applications. Pathogens. 11: 777.","pubmedId":"","doi":"10.3390/pathogens11070777"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. Jiang2014.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
","pubmedId":"","doi":"10.1093/bioinformatics/btm039"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide. Nucleic Acids Res. 32: 11-16.","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17: 10.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Jacobs Sera D. 2018. Annotation of bacteriophage genome sequences using DNA Master: An overview. Methods Mol. Biol. 1681: 217-229.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN: Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Russell2018.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Sambrook J, Russell DW. 2006. Purification of nucleic acids by extraction with phenol:chloroform. CSH Protoc. 2006: db.prot4455.","pubmedId":"","doi":"10.1101/pdb.prot4455"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long. PLoS Comput. Biol. 13: e1005595.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, et al., Alva V. 2018. undefined. Computation Resources for Molecular Biology. 430: 2237.","pubmedId":"","doi":"https://doi.org/10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Zorawik2024.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Sequence Analysis of two B1 Mycobacteriophages, ElvisPhasley and Mesmerelda
","reviews":[{"reviewer":{"displayName":"Sally Molloy"},"openAcknowledgement":false,"status":{"submitted":true}},{"reviewer":{"displayName":"Dan Williams"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"05c267cb-b620-4617-a444-62267476f716","decision":"accept","abstract":"Mycobacteriophages ElvisPhasley and Mesmerelda were isolated from soil and infect Mycobacterium smegmatis. Each phage has siphovirus morphology and encodes 102 genes. Based on broader genomic similarity to actinobacteriophages, both are assigned to the B1 subcluster.
","acknowledgements":"We thank the University of Pittsburgh for genome sequencing, Old Dominion University Applied Research Center for the TEM images, the Hatfull lab, and the entire SEA-PHAGES program for their considerable ongoing support. We also thank the many institutions with SEA-PHAGES programs for their discovery and annotation of phages which made the Gepard plot in Figure 1f possible.
","authors":[{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"vafiggins@wm.edu","firstName":"Victoria","lastName":"Figgins","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"gehussey@wm.edu","firstName":"Grace","lastName":"Hussey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","writing_originalDraft","writing_reviewEditing"],"email":"shaimowitz@wm.edu","firstName":"Sarah","lastName":"Haimowitz","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"vpande@wm.edu","firstName":"Vera","lastName":"Pande","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"moroyster@wm.edu","firstName":"Marcus","lastName":"Royster","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egflanagan@wm.edu","firstName":"Emmery","lastName":"Flanagan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"mefountain@wm.edu","firstName":"Me'Shar'li'a","lastName":"Fountain","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egeorge@wm.edu","firstName":"Erin","lastName":"George","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zmherring@wm.edu","firstName":"Zion","lastName":"Herring","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"smjensen@wm.edu","firstName":"Scarlett","lastName":"Jensen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"jnnguyen@wm.edu","firstName":"Jenny","lastName":"Nguyen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"klonufer@wm.edu","firstName":"Konur","lastName":"Onufer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"plsmith02@wm.edu","firstName":"Phoenix","lastName":"Smith","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"bfstrong@wm.edu","firstName":"Brennan","lastName":"Strong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zwang64@wm.edu","firstName":"Bruce","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"ayang02@wm.edu","firstName":"Abigail","lastName":"Yang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","validation","writing_reviewEditing","visualization"],"email":"hlqian@wm.edu","firstName":"Heather","lastName":"Qian","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary"],"departments":["Department of Applied Science"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","project","resources","supervision","validation","visualization","writing_originalDraft","writing_reviewEditing","fundingAcquisition"],"email":"mssaha@wm.edu","firstName":"Margaret","lastName":"Saha","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-0096-2667"}],"awards":[{"awardId":"1R15HD096415-01 ","funderName":"National Institutes of Health (United States)","awardRecipient":"Margaret Saha"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"","image":{"url":"https://portal.micropublication.org/uploads/8326d1e514704e97e897c4c193440fb1.jpg"},"imageCaption":"Fig. 1 Plaque morphologies of ElvisPhasley (a) and Mesmerelda (b). ElvisPhasley forms clear plaques with translucent halos, and Mesmerelda forms clear plaques. Scale bars for plaque images are 12.5 mm. Negative stain (uranyl acetate, 1%) transmission electron microscopy (TEM) of ElvisPhasley (c) and Mesmerelda (d) revealing siphoviral morphology. Scale bars for micrographs are 50 nm. (e) Alignment of ElvisPhasley and Mesmerelda genomes using Phamerator. The genome is represented by the ruler, in kilo base pairs, with boxes above and below the ruler representing forward and reverse transcribed genes, respectively, and gene numbers presented within the box. (f) Gepard plot comparing the genomic sequences of 40 B1 cluster phages, including ElvisPhasley and Mesmerelda, and 10 B2 cluster phages. Both axes represent all 50 phage genomes, and each diagonal line on the dot plot represents high nucleotide identity between phage genome sequences. The Gepard plot exemplifies the genomic similarities of ElvisPhasley and Mesmerelda to other B1 cluster phages and the genomic dissimilarity of ElvisPhasley and Mesmerelda to B2 cluster phages.
","imageTitle":"Plaque and TEM Images and Genomic Organization of ElvisPhasely and Mesmerelda
","methods":"","reagents":"","patternDescription":"Advancing the characterization of mycobacteriophages, bacteriophages that infect Mycobacterium hosts, is of interest due to increasing antibiotic resistance in pathogenic Mycobacterium species (Hatfull, 2020; Hatfull, 2022; Bonacorsi et al., 2024). Mycobacteriophage engineering is a promising approach in the detection and treatment of mycobacterial infections (Bonacorsi et al., 2024; Hosseiniporgham et al., 2022). Therefore, the continued characterization of mycobacteriophages broadens the capabilities of bioengineers in combating this global issue. Here, we report the genome sequences of two novel mycobacteriophages, ElvisPhasley and Mesmerelda.
Phages were isolated from two different soil samples: ElvisPhasley from wet, silty soil on the William & Mary campus in Williamsburg, VA; Mesmerelda from a bag of commercially available garden soil (Table 1). A standard enrichment procedure was followed for both samples: 5 g of each sample was suspended in 45 mL of 7H9 media, inoculated with Mycobacterium smegmatis mc2 155, and incubated in a 37°C shaker at 250 rpm for 48 hours (Zorawik et al., 2024). Resultant cultures were filtered using a 0.22-µm filter, and filtrates were plated in 7H9 top agar with M. smegmatis mc2 155. After 24-48 hours, both ElvisPhasley and Mesmerelda produced clear plaques (Fig. 1a-b). Both phages were purified with three rounds of plating, and a high titer lysate was prepared by flooding plates exhibiting nearly confluent bacterial lysis with phage buffer (10 mM Tris, pH 7.5; 10 mM MgSO4; 68 mM NaCl; 1 mM CaCl2). Negative stain (1% uranyl acetate) transmission electron microscopy of each lysate revealed siphovirus morphology for both phages (Fig. 1c-d).
Phage DNA was extracted from each high titer lysate using a phenol-chloroform-isoamyl alcohol procedure and ethanol precipitation (Sambrook and Russell, 2006). DNA was prepared for sequencing using the NEB Ultra II Library Kit and sequenced using an Illumina NextSeq 1000 sequencer (single-end, 100 base read). Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) (Martin, 2011; Jiang et al., 2014; Wick et al., 2017). Newbler (v.2.9) was then used to assemble the genome and Consed (v.29) to check for completeness (Russell, 2018; Gordon et al., 1998). Sequencing data and genome characteristics are presented in Table 1.
Genome annotation was performed using DNA Master (v.5.23.6) and PECAAN (v.20221109) (Rinehart et al., 2016; Pope and Jacobs-Sera, 2018). Start sites of protein coding genes were predicted using Glimmer (v.3.02) and GeneMark (v.2.5) (Besemer and Borodovsky, 2005; Delcher et al., 2007. These predictions were manually refined using GeneMark coding potential predictions (Besemer and Borodovsky, 2005), start site similarity comparisons between pham members obtained from Starterator (http://phages.wustl.edu/starterator/), and start site alignment scores with homologous genes found using BLASTp against the NCBI non-redundant protein and Actinobacteriophage databases (Altschul et al., 1990). No tRNAs were predicted using Aragorn (v.1.2.41) and tRNAscan (Laslett and Canback, 2004; Lowe and Eddy, 1997).
Predictions from HHPred (using the PDB_mmCIF70, NCBI_CD, SCOPe70, and pFAM-A databases), BLASTp, and Phamerator for highly similar genes were used to assign putative gene functions (Cresawn et al., 2011; Zimmermann et al., 2018). Both phages are assigned to cluster B, subcluster B1 using the gene content similarity (GCS) tool at the Actinobacteriophage database, PhagesDB, and clustering parameters of at least 35% GCS to actinobacteriophages (Russell and Hatfull, 2017). Default settings were used for all software.
The genomes of ElvisPhasley and Mesmerelda both encode 102 protein-coding genes, with 33 and 32 genes, respectively, assigned functions involved in virion propagation, structure, and lysis (Fig. 1e). As neither ElvisPhasley nor Mesmerelda encode a putative integrase or other proteins implicated in lysogeny, these phages are predicted to be virulent. Both ElvisPhasley and Mesmerelda display strong genomic similarity to other B1 subcluster phages and genomic dissimilarity to B2 subcluster phages as displayed on a Gepard dot plot (Fig. 1f; Krumsiek et al., 2007). ElvisPhasley shares 89.22% GCS with its closest relative, OSMaximus (Russell and Hatfull, 2017). At the nucleotide level, ElvisPhasley shares 99.00% identity with OSMaximus over 97% coverage (BLAST). Within this covered region, we identified 968 nucleotide differences, 249 of which were found in coding regions. Of these differences, 238 resulted in amino acid substitutions, 98 of which were conservative and 140 of which were non-conservative as classified by the BLOSUM62 alignment score matrix. Likewise, Mesmerelda shares 95.1% GCS with its closest relative, Orfeu (Russell and Hatfull, 2017). These phages share 99.16% nucleotide identity over 100% coverage. Of the 557 nucleotide differences, 136 differences occur in coding regions. These differences result in 115 amino acid substitutions, 53 of which are conservative and 62 of which are not conservative.
Nucleotide sequence accession numbers
ElvisPhasley and Mesmerelda are available at GenBank with Accession No. PV876949 and PV876954, and Sequence Read Archive (SRA) No. SRX29990110 and SRX29990101.
Table 1: Genome and sequencing information for Mesmerelda and ElvisPhasley
Phage | ElvisPhasley | Mesmerelda |
Isolation GPS coordinates | 37° 16' 13.4034\" N 76° 43' 3.216\" W | 37° 16' 11.8992\" N 76° 42' 52.5996\" W |
Morphology | Siphovirus | Siphovirus |
Average capsid diameter (± SD) | 60 ± 4 nm (n = 5) | 50 ± 4 nm (n = 5) |
Average tail length (± SD) | 310 ± 10 nm (n = 5) | 220 ± 10 nm (n = 5) |
Sequencing reads | 4,697,092 | 4,305,175 |
Sequencing coverage, fold | 6,513 | 5,969 |
Genome length (bp) | 69,502 | 68,890 |
Character of genome ends | Circularly permuted | Circularly permuted |
Number of protein-coding genes | 102 | 102 |
GC content (%) | 66.4 | 66.4 |
Accession number | ||
SRA |
Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Bonacorsi A, Ferretti C, Di Luca M, Rindi L. 2024. Mycobacteriophages and Their Applications. Antibiotics. 13: 926.","pubmedId":"","doi":"10.3390/antibiotics13100926"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. Cresawn2011.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, dynamics, and applications. Annu. Rev. Virol. 7: 37-61.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF. 2022. Mycobacteriophages: From Petri dish to patient. PLoS Pathog. 18: e1010602.","pubmedId":"","doi":"10.1371/journal.ppat.1010602"},{"reference":"Hosseiniporgham S, Sechi LA. 2022. A Review on Mycobacteriophages: From Classification to Applications. Pathogens. 11: 777.","pubmedId":"","doi":"10.3390/pathogens11070777"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. Jiang2014.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
","pubmedId":"","doi":"10.1093/bioinformatics/btm039"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide. Nucleic Acids Res. 32: 11-16.","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17: 10.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Jacobs Sera D. 2018. Annotation of bacteriophage genome sequences using DNA Master: An overview. Methods Mol. Biol. 1681: 217-229.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN: Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Russell2018.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Sambrook J, Russell DW. 2006. Purification of nucleic acids by extraction with phenol:chloroform. CSH Protoc. 2006: db.prot4455.","pubmedId":"","doi":"10.1101/pdb.prot4455"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long. PLoS Comput. Biol. 13: e1005595.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, et al., Alva V. 2018. undefined. Computation Resources for Molecular Biology. 430: 2237.","pubmedId":"","doi":"https://doi.org/10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Zorawik2024.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Sequence Analysis of Two B1 Mycobacteriophages, ElvisPhasley and Mesmerelda
","reviews":[],"curatorReviews":[]},{"id":"00b4cdc8-153f-4811-99d1-d7fc66c13107","decision":"edit","abstract":"Mycobacteriophages ElvisPhasley and Mesmerelda were isolated from soil and infect Mycobacterium smegmatis. Each phage has siphovirus morphology and encodes 102 genes. Based on broader genomic similarity to actinobacteriophages, both are assigned to the B1 subcluster.
","acknowledgements":"We thank the University of Pittsburgh for genome sequencing, Old Dominion University Applied Research Center for the TEM images, the Hatfull lab, and the entire SEA-PHAGES program for their considerable ongoing support. We also thank the many institutions with SEA-PHAGES programs for their discovery and annotation of phages which made the Gepard plot in Figure 1f possible.
","authors":[{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"vafiggins@wm.edu","firstName":"Victoria","lastName":"Figgins","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"gehussey@wm.edu","firstName":"Grace","lastName":"Hussey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","writing_originalDraft","writing_reviewEditing"],"email":"shaimowitz@wm.edu","firstName":"Sarah","lastName":"Haimowitz","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"vpande@wm.edu","firstName":"Vera","lastName":"Pande","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"moroyster@wm.edu","firstName":"Marcus","lastName":"Royster","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egflanagan@wm.edu","firstName":"Emmery","lastName":"Flanagan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"mefountain@wm.edu","firstName":"Me'Shar'li'a","lastName":"Fountain","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egeorge@wm.edu","firstName":"Erin","lastName":"George","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zmherring@wm.edu","firstName":"Zion","lastName":"Herring","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"smjensen@wm.edu","firstName":"Scarlett","lastName":"Jensen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"jnnguyen@wm.edu","firstName":"Jenny","lastName":"Nguyen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"klonufer@wm.edu","firstName":"Konur","lastName":"Onufer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"plsmith02@wm.edu","firstName":"Phoenix","lastName":"Smith","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"bfstrong@wm.edu","firstName":"Brennan","lastName":"Strong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zwang64@wm.edu","firstName":"Bruce","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"ayang02@wm.edu","firstName":"Abigail","lastName":"Yang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","validation","writing_reviewEditing","visualization"],"email":"hlqian@wm.edu","firstName":"Heather","lastName":"Qian","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William and Mary, Williamsburg, VA USA"],"departments":["Department of Applied Science"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","project","resources","supervision","validation","visualization","writing_originalDraft","writing_reviewEditing","fundingAcquisition"],"email":"mssaha@wm.edu","firstName":"Margaret","lastName":"Saha","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-0096-2667"}],"awards":[{"awardId":"1R15HD096415-01 ","funderName":"National Institutes of Health (United States)","awardRecipient":"Margaret Saha"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"","image":{"url":"https://portal.micropublication.org/uploads/8326d1e514704e97e897c4c193440fb1.jpg"},"imageCaption":"Fig. 1 Plaque morphologies of ElvisPhasley (a) and Mesmerelda (b). ElvisPhasley forms clear plaques with translucent halos, and Mesmerelda forms clear plaques. Scale bars for plaque images are 12.5 mm. Negative stain (uranyl acetate, 1%) transmission electron microscopy (TEM) of ElvisPhasley (c) and Mesmerelda (d) revealing siphoviral morphology. Scale bars for micrographs are 50 nm. (e) Alignment of ElvisPhasley and Mesmerelda genomes using Phamerator. The genome is represented by the ruler, in kilo base pairs, with boxes above and below the ruler representing forward and reverse transcribed genes, respectively, and gene numbers presented within the box. (f) Gepard plot comparing the genomic sequences of 40 B1 cluster phages, including ElvisPhasley and Mesmerelda, and 10 B2 cluster phages. Both axes represent all 50 phage genomes, and each diagonal line on the dot plot represents high nucleotide identity between phage genome sequences. The Gepard plot exemplifies the genomic similarities of ElvisPhasley and Mesmerelda to other B1 cluster phages and the genomic dissimilarity of ElvisPhasley and Mesmerelda to B2 cluster phages.
","imageTitle":"Plaque and TEM Images and Genomic Organization of ElvisPhasley and Mesmerelda
","methods":"","reagents":"","patternDescription":"Advancing the characterization of mycobacteriophages, bacteriophages that infect Mycobacterium hosts, is of interest due to increasing antibiotic resistance in pathogenic Mycobacterium species (Hatfull, 2020; Hatfull, 2022; Bonacorsi et al., 2024). Mycobacteriophage engineering is a promising approach in the detection and treatment of mycobacterial infections (Bonacorsi et al., 2024; Hosseiniporgham et al., 2022). Therefore, the continued characterization of mycobacteriophages broadens the capabilities of bioengineers in combating this global issue. Here, we report the genome sequences of two novel mycobacteriophages, ElvisPhasley and Mesmerelda.
Phages were isolated from two different soil samples: ElvisPhasley from wet, silty soil on the William & Mary campus in Williamsburg, VA; Mesmerelda from a bag of commercially available garden soil (Table 1). A standard enrichment procedure was followed for both samples: 5 g of each sample was suspended in 45 mL of 7H9 media, inoculated with Mycobacterium smegmatis mc2 155, and incubated in a 37°C shaker at 250 rpm for 48 hours (Zorawik et al., 2024). Resultant cultures were filtered using a 0.22-µm filter, and filtrates were plated in 7H9 top agar with M. smegmatis mc2 155. After 24-48 hours, both ElvisPhasley and Mesmerelda produced clear plaques (Fig. 1a-b). Both phages were purified with three rounds of plating, and a high titer lysate was prepared by flooding plates exhibiting nearly confluent bacterial lysis with phage buffer (10 mM Tris, pH 7.5; 10 mM MgSO4; 68 mM NaCl; 1 mM CaCl2). Negative stain (1% uranyl acetate) transmission electron microscopy of each lysate revealed siphovirus morphology for both phages (Fig. 1c-d).
Phage DNA was extracted from each high titer lysate using a phenol-chloroform-isoamyl alcohol procedure and ethanol precipitation (Sambrook and Russell, 2006). DNA was prepared for sequencing using the NEB Ultra II Library Kit and sequenced using an Illumina NextSeq 1000 sequencer (single-end, 100 base read). Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) (Martin, 2011; Jiang et al., 2014; Wick et al., 2017). Newbler (v.2.9) was then used to assemble the genome and Consed (v.29) to check for completeness (Russell, 2018; Gordon et al., 1998). Sequencing data and genome characteristics are presented in Table 1.
Genome annotation was performed using DNA Master (v.5.23.6) and PECAAN (v.20221109) (Rinehart et al., 2016; Pope and Jacobs-Sera, 2018). Start sites of protein coding genes were predicted using Glimmer (v.3.02) and GeneMark (v.2.5) (Besemer and Borodovsky, 2005; Delcher et al., 2007). These predictions were manually refined using GeneMark coding potential predictions (Besemer and Borodovsky, 2005), start site similarity comparisons between pham members obtained from Starterator (http://phages.wustl.edu/starterator/), and start site alignment scores with homologous genes found using BLASTp against the NCBI non-redundant protein and Actinobacteriophage databases (Altschul et al., 1990). No tRNAs were predicted using Aragorn (v.1.2.41) and tRNAscan (Laslett and Canback, 2004; Lowe and Eddy, 1997).
Predictions from HHPred (using the PDB_mmCIF70, NCBI_CD, SCOPe70, and pFAM-A databases), BLASTp, and Phamerator for highly similar genes were used to assign putative gene functions (Cresawn et al., 2011; Zimmermann et al., 2018). Both phages are assigned to cluster B, subcluster B1 using the gene content similarity (GCS) tool at the Actinobacteriophage database, PhagesDB, and clustering parameters of at least 35% GCS to actinobacteriophages (Russell and Hatfull, 2017). Default settings were used for all software.
The genomes of ElvisPhasley and Mesmerelda both encode 102 protein-coding genes, with 33 and 32 genes, respectively, assigned functions involved in virion propagation, structure, and lysis (Fig. 1e). As neither ElvisPhasley nor Mesmerelda encode a putative integrase or other proteins implicated in lysogeny, these phages are predicted to be virulent. Both ElvisPhasley and Mesmerelda display strong genomic similarity to other B1 subcluster phages and genomic dissimilarity to B2 subcluster phages as displayed on a Gepard dot plot (Fig. 1f; Krumsiek et al., 2007). ElvisPhasley shares 89.22% GCS with its closest relative, OSMaximus (Russell and Hatfull, 2017). At the nucleotide level, ElvisPhasley shares 99.00% identity with OSMaximus over 97% coverage (BLAST). Within this covered region, we identified 968 nucleotide differences, 249 of which were found in coding regions. Of these differences, 238 resulted in amino acid substitutions, 98 of which were conservative and 140 of which were non-conservative as classified by the BLOSUM62 alignment score matrix. Likewise, Mesmerelda shares 95.1% GCS with its closest relative, Orfeu (Russell and Hatfull, 2017). These phages share 99.16% nucleotide identity over 100% coverage. Of the 557 nucleotide differences, 136 differences occur in coding regions. These differences result in 115 amino acid substitutions, 53 of which are conservative and 62 of which are not conservative.
Nucleotide sequence accession numbers
ElvisPhasley and Mesmerelda are available at GenBank with Accession No. PV876949 and PV876954, and Sequence Read Archive (SRA) No. SRX29990110 and SRX29990101.
Table 1: Genome and sequencing information for Mesmerelda and ElvisPhasley
Phage | ElvisPhasley | Mesmerelda |
Isolation GPS coordinates | 37° 16' 13.4034\" N 76° 43' 3.216\" W | 37° 16' 11.8992\" N 76° 42' 52.5996\" W |
Morphology | Siphovirus | Siphovirus |
Average capsid diameter (± SD) | 60 ± 4 nm (n = 5) | 50 ± 4 nm (n = 5) |
Average tail length (± SD) | 310 ± 10 nm (n = 5) | 220 ± 10 nm (n = 5) |
Sequencing reads | 4,697,092 | 4,305,175 |
Sequencing coverage, fold | 6,513 | 5,969 |
Genome length (bp) | 69,502 | 68,890 |
Character of genome ends | Circularly permuted | Circularly permuted |
Number of protein-coding genes | 102 | 102 |
GC content (%) | 66.4 | 66.4 |
Accession number | ||
SRA |
Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Bonacorsi A, Ferretti C, Di Luca M, Rindi L. 2024. Mycobacteriophages and Their Applications. Antibiotics. 13: 926.","pubmedId":"","doi":"10.3390/antibiotics13100926"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. Cresawn2011.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, dynamics, and applications. Annu. Rev. Virol. 7: 37-61.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF. 2022. Mycobacteriophages: From Petri dish to patient. PLoS Pathog. 18: e1010602.","pubmedId":"","doi":"10.1371/journal.ppat.1010602"},{"reference":"Hosseiniporgham S, Sechi LA. 2022. A Review on Mycobacteriophages: From Classification to Applications. Pathogens. 11: 777.","pubmedId":"","doi":"10.3390/pathogens11070777"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. Jiang2014.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
","pubmedId":"","doi":"10.1093/bioinformatics/btm039"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide. Nucleic Acids Res. 32: 11-16.","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17: 10.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Jacobs Sera D. 2018. Annotation of bacteriophage genome sequences using DNA Master: An overview. Methods Mol. Biol. 1681: 217-229.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN: Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Russell2018.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Sambrook J, Russell DW. 2006. Purification of nucleic acids by extraction with phenol:chloroform. CSH Protoc. 2006: db.prot4455.","pubmedId":"","doi":"10.1101/pdb.prot4455"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long. PLoS Comput. Biol. 13: e1005595.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, et al., Alva V. 2018. undefined. Computation Resources for Molecular Biology. 430: 2237.","pubmedId":"","doi":"https://doi.org/10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Zorawik2024.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Sequence Analysis of Two B1 Mycobacteriophages, ElvisPhasley and Mesmerelda
","reviews":[],"curatorReviews":[]},{"id":"822a9c91-d20e-4238-8fe6-b78739b690af","decision":"publish","abstract":"Mycobacteriophages ElvisPhasley and Mesmerelda were isolated from soil and infect Mycobacterium smegmatis. Each phage has siphovirus morphology and encodes 102 genes. Based on broader genomic similarity to actinobacteriophages, both are assigned to the B1 subcluster.
","acknowledgements":"We thank the University of Pittsburgh for genome sequencing, Old Dominion University Applied Research Center for the TEM images, the Hatfull lab, and the entire SEA-PHAGES program for their considerable ongoing support. We also thank the many institutions with SEA-PHAGES programs for their discovery and annotation of phages which made the Gepard plot in Figure 1f possible.
","authors":[{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"vafiggins@wm.edu","firstName":"Victoria","lastName":"Figgins","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","visualization","writing_originalDraft","writing_reviewEditing"],"email":"gehussey@wm.edu","firstName":"Grace","lastName":"Hussey","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["dataCuration","formalAnalysis","investigation","validation","writing_originalDraft","writing_reviewEditing"],"email":"shaimowitz@wm.edu","firstName":"Sarah","lastName":"Haimowitz","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"vpande@wm.edu","firstName":"Vera","lastName":"Pande","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"moroyster@wm.edu","firstName":"Marcus","lastName":"Royster","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egflanagan@wm.edu","firstName":"Emmery","lastName":"Flanagan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"mefountain@wm.edu","firstName":"Me'Shar'li'a","lastName":"Fountain","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"egeorge@wm.edu","firstName":"Erin","lastName":"George","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zmherring@wm.edu","firstName":"Zion","lastName":"Herring","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"smjensen@wm.edu","firstName":"Scarlett","lastName":"Jensen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"jnnguyen@wm.edu","firstName":"Jenny","lastName":"Nguyen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"klonufer@wm.edu","firstName":"Konur","lastName":"Onufer","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"plsmith02@wm.edu","firstName":"Phoenix","lastName":"Smith","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"bfstrong@wm.edu","firstName":"Brennan","lastName":"Strong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"zwang64@wm.edu","firstName":"Bruce","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"ayang02@wm.edu","firstName":"Abigail","lastName":"Yang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["formalAnalysis","validation","writing_reviewEditing","visualization"],"email":"hlqian@wm.edu","firstName":"Heather","lastName":"Qian","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["William & Mary, Williamsburg, VA, US"],"departments":["Department of Applied Science"],"credit":["conceptualization","dataCuration","formalAnalysis","investigation","project","resources","supervision","validation","visualization","writing_originalDraft","writing_reviewEditing","fundingAcquisition"],"email":"mssaha@wm.edu","firstName":"Margaret","lastName":"Saha","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0003-0096-2667"}],"awards":[{"awardId":"1R15HD096415-01 ","funderName":"National Institutes of Health (United States)","awardRecipient":"Margaret Saha"}],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"","image":{"url":"https://portal.micropublication.org/uploads/8326d1e514704e97e897c4c193440fb1.jpg"},"imageCaption":"Fig. 1 Plaque morphologies of ElvisPhasley (a) and Mesmerelda (b). ElvisPhasley forms clear plaques with translucent halos, and Mesmerelda forms clear plaques. Scale bars for plaque images are 12.5 mm. Negative stain (uranyl acetate, 1%) transmission electron microscopy (TEM) of ElvisPhasley (c) and Mesmerelda (d) revealing siphoviral morphology. Scale bars for micrographs are 50 nm. (e) Alignment of ElvisPhasley and Mesmerelda genomes using Phamerator. The genome is represented by the ruler, in kilo base pairs, with boxes above and below the ruler representing forward and reverse transcribed genes, respectively, and gene numbers presented within the box. (f) Gepard plot comparing the genomic sequences of 40 B1 cluster phages, including ElvisPhasley and Mesmerelda, and 10 B2 cluster phages. Both axes represent all 50 phage genomes, and each diagonal line on the dot plot represents high nucleotide identity between phage genome sequences. The Gepard plot exemplifies the genomic similarities of ElvisPhasley and Mesmerelda to other B1 cluster phages and the genomic dissimilarity of ElvisPhasley and Mesmerelda to B2 cluster phages.
","imageTitle":"Plaque and TEM Images and Genomic Organization of ElvisPhasley and Mesmerelda
","methods":"","reagents":"","patternDescription":"Advancing the characterization of mycobacteriophages, bacteriophages that infect Mycobacterium hosts, is of interest due to increasing antibiotic resistance in pathogenic Mycobacterium species (Hatfull, 2020; Hatfull, 2022; Bonacorsi et al., 2024). Mycobacteriophage engineering is a promising approach in the detection and treatment of mycobacterial infections (Bonacorsi et al., 2024; Hosseiniporgham et al., 2022). Therefore, the continued characterization of mycobacteriophages broadens the capabilities of bioengineers in combating this global issue. Here, we report the genome sequences of two novel mycobacteriophages, ElvisPhasley and Mesmerelda.
Phages were isolated from two different soil samples: ElvisPhasley from wet, silty soil on the William & Mary campus in Williamsburg, VA; Mesmerelda from a bag of commercially available garden soil (Table 1). A standard enrichment procedure was followed for both samples: 5 g of each sample was suspended in 45 mL of 7H9 media, inoculated with Mycobacterium smegmatis mc2 155, and incubated in a 37°C shaker at 250 rpm for 48 hours (Zorawik et al., 2024). Resultant cultures were filtered using a 0.22-µm filter, and filtrates were plated in 7H9 top agar with M. smegmatis mc2 155. After 24-48 hours, both ElvisPhasley and Mesmerelda produced clear plaques (Fig. 1a-b). Both phages were purified with three rounds of plating, and a high titer lysate was prepared by flooding plates exhibiting nearly confluent bacterial lysis with phage buffer (10 mM Tris, pH 7.5; 10 mM MgSO4; 68 mM NaCl; 1 mM CaCl2). Negative stain (1% uranyl acetate) transmission electron microscopy of each lysate revealed siphovirus morphology for both phages (Fig. 1c-d).
Phage DNA was extracted from each high titer lysate using a phenol-chloroform-isoamyl alcohol procedure and ethanol precipitation (Sambrook and Russell, 2006). DNA was prepared for sequencing using the NEB Ultra II Library Kit and sequenced using an Illumina NextSeq 1000 sequencer (single-end, 100 base read). Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) (Martin, 2011; Jiang et al., 2014; Wick et al., 2017). Newbler (v.2.9) was then used to assemble the genome and Consed (v.29) to check for completeness (Russell, 2018; Gordon et al., 1998). Sequencing data and genome characteristics are presented in Table 1.
Genome annotation was performed using DNA Master (v.5.23.6) and PECAAN (v.20221109) (Rinehart et al., 2016; Pope and Jacobs-Sera, 2018). Start sites of protein coding genes were predicted using Glimmer (v.3.02) and GeneMark (v.2.5) (Besemer and Borodovsky, 2005; Delcher et al., 2007). These predictions were manually refined using GeneMark coding potential predictions (Besemer and Borodovsky, 2005), start site similarity comparisons between pham members obtained from Starterator (http://phages.wustl.edu/starterator/), and start site alignment scores with homologous genes found using BLASTp against the NCBI non-redundant protein and Actinobacteriophage databases (Altschul et al., 1990). No tRNAs were predicted using Aragorn (v.1.2.41) and tRNAscan (Laslett and Canback, 2004; Lowe and Eddy, 1997).
Predictions from HHPred (using the PDB_mmCIF70, NCBI_CD, SCOPe70, and pFAM-A databases), BLASTp, and Phamerator for highly similar genes were used to assign putative gene functions (Cresawn et al., 2011; Zimmermann et al., 2018). Both phages are assigned to cluster B, subcluster B1 using the gene content similarity (GCS) tool at the Actinobacteriophage database, PhagesDB, and clustering parameters of at least 35% GCS to actinobacteriophages (Russell and Hatfull, 2017). Default settings were used for all software.
The genomes of ElvisPhasley and Mesmerelda both encode 102 protein-coding genes, with 33 and 32 genes, respectively, assigned functions involved in virion propagation, structure, and lysis (Fig. 1e). As neither ElvisPhasley nor Mesmerelda encode a putative integrase or other proteins implicated in lysogeny, these phages are predicted to be virulent. Both ElvisPhasley and Mesmerelda display strong genomic similarity to other B1 subcluster phages and genomic dissimilarity to B2 subcluster phages as displayed on a Gepard dot plot (Fig. 1f; Krumsiek et al., 2007). ElvisPhasley shares 89.22% GCS with its closest relative, OSMaximus (Russell and Hatfull, 2017). At the nucleotide level, ElvisPhasley shares 99.00% identity with OSMaximus over 97% coverage (BLAST). Within this covered region, we identified 968 nucleotide differences, 249 of which were found in coding regions. Of these differences, 238 resulted in amino acid substitutions, 98 of which were conservative and 140 of which were non-conservative as classified by the BLOSUM62 alignment score matrix. Likewise, Mesmerelda shares 95.1% GCS with its closest relative, Orfeu (Russell and Hatfull, 2017). These phages share 99.16% nucleotide identity over 100% coverage. Of the 557 nucleotide differences, 136 differences occur in coding regions. These differences result in 115 amino acid substitutions, 53 of which are conservative and 62 of which are not conservative.
Nucleotide sequence accession numbers
ElvisPhasley and Mesmerelda are available at GenBank with Accession No. PV876949 and PV876954, and Sequence Read Archive (SRA) No. SRX29990110 and SRX29990101.
Table 1: Genome and sequencing information for Mesmerelda and ElvisPhasley
Phage | ElvisPhasley | Mesmerelda |
Isolation GPS coordinates | 37° 16' 13.4034\" N 76° 43' 3.216\" W | 37° 16' 11.8992\" N 76° 42' 52.5996\" W |
Morphology | Siphovirus | Siphovirus |
Average capsid diameter (± SD) | 60 ± 4 nm (n = 5) | 50 ± 4 nm (n = 5) |
Average tail length (± SD) | 310 ± 10 nm (n = 5) | 220 ± 10 nm (n = 5) |
Sequencing reads | 4,697,092 | 4,305,175 |
Sequencing coverage, fold | 6,513 | 5,969 |
Genome length (bp) | 69,502 | 68,890 |
Character of genome ends | Circularly permuted | Circularly permuted |
Number of protein-coding genes | 102 | 102 |
GC content (%) | 66.4 | 66.4 |
Accession number | ||
SRA |
Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Bonacorsi A, Ferretti C, Di Luca M, Rindi L. 2024. Mycobacteriophages and Their Applications. Antibiotics. 13: 926.","pubmedId":"","doi":"10.3390/antibiotics13100926"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. Cresawn2011.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, dynamics, and applications. Annu. Rev. Virol. 7: 37-61.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF. 2022. Mycobacteriophages: From Petri dish to patient. PLoS Pathog. 18: e1010602.","pubmedId":"","doi":"10.1371/journal.ppat.1010602"},{"reference":"Hosseiniporgham S, Sechi LA. 2022. A Review on Mycobacteriophages: From Classification to Applications. Pathogens. 11: 777.","pubmedId":"","doi":"10.3390/pathogens11070777"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. Jiang2014.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Krumsiek J, Arnold R, Rattei T. 2007. Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
","pubmedId":"","doi":"10.1093/bioinformatics/btm039"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide. Nucleic Acids Res. 32: 11-16.","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17: 10.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Jacobs Sera D. 2018. Annotation of bacteriophage genome sequences using DNA Master: An overview. Methods Mol. Biol. 1681: 217-229.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN: Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Russell2018.","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Sambrook J, Russell DW. 2006. Purification of nucleic acids by extraction with phenol:chloroform. CSH Protoc. 2006: db.prot4455.","pubmedId":"","doi":"10.1101/pdb.prot4455"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long. PLoS Comput. Biol. 13: e1005595.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kubler J, Lozajic M, et al., Alva V. 2018. undefined. Computation Resources for Molecular Biology. 430: 2237.","pubmedId":"","doi":"https://doi.org/10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Zorawik2024.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Sequence Analysis of Two B1 Mycobacteriophages, ElvisPhasley and Mesmerelda
","reviews":[],"curatorReviews":[]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aegorhinus vitulus","label":"Aegorhinus vitulus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alaimidae","label":"Alaimidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"allobates femoralis","label":"Allobates femoralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alnus glutinosa","label":"Alnus glutinosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa aestivalis","label":"Alosa aestivalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa pseudoharengus","label":"Alosa pseudoharengus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alternaria alternata","label":"Alternaria alternata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"amynthas agrestis","label":"Amynthas Agrestis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma caninum","label":"Ancylostoma caninum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma ceylanicum","label":"Ancylostoma ceylanicum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anemone multifida","label":"Anemone multifida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anguilla rostrata","label":"Anguilla rostrata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anisakis simplex","label":"Anisakis simplex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anomala albopilosa","label":"Anomala albopilosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arabidopsis","label":"Arabidopsis","imageSrc":"arabidopsis.png","imageAlt":"Arabidopsis graphic by Zoe Zorn CC BY 4.0","mod":"TAIR","modLink":"https://arabidopsis.org","linkVariable":""},{"value":"architeuthis dux","label":"Architeuthis dux","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arion vulgaris","label":"Arion vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"armeria","label":"Armeria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"artemia","label":"Artemia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arthrobacter sp.","label":"Arthrobacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia","label":"Ascaridia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia galli","label":"Ascaridia galli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"asparagopsis taxiformis","label":"Asparagopsis taxiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"astatotilapia burtoni","label":"Astatotilapia burtoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"avena sativa","label":"Avena sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aves","label":"Aves","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus","label":"Bacillus (firmicutes)","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus cereus","label":"Bacillus cereus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus mycoides","label":"Bacillus mycoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus subtilis","label":"Bacillus subtilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus thuringiensis","label":"Bacillus thuringiensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus toyonensis","label":"Bacillus toyonensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus wiedmannii","label":"Bacillus wiedmannii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteria","label":"Bacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteriophage","label":"Bacteriophage","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bactrocera","label":"Bactrocera sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"batrachospermum gelatinosum","label":"Batrachospermum gelatinosum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula lenta","label":"Betula lenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula nigra","label":"Betula nigra","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus dahlbohmii","label":"Bombus dahlbohmii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus terrestris","label":"Bombus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombyx mori","label":"Bombyx mori","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bos taurus","label":"Bos Taurus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brachygobius doriae","label":"Brachygobius doriae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica oleracea","label":"Brassica oleracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica rapa","label":"Brassica rapa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brugia malayi","label":"Brugia malayi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"burkholderia thailandensis","label":"Burkholderia thailandensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"buttiauxella","label":"Buttiauxella","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis brenneri","label":"Caenorhabditis brenneri","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis briggsae","label":"Caenorhabditis briggsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"c. elegans","label":"Caenorhabditis elegans","imageSrc":"c-elegans.jpg","imageAlt":"C. elegans graphic by Zoe Zorn CC BY 4.0","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"caenorhabditis inopinata","label":"Caenorhabditis inopinata","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis japonica","label":"Caenorhabditis japonica","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis nigoni","label":"Caenorhabditis nigoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis remanei","label":"Caenorhabditis remanei","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis tropicalis","label":"Caenorhabditis tropicalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus","label":"Calidifontibacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus erzuremensis","label":"Calidifontibacillus erzuremensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calliphora sp","label":"Calliphora sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caltha sagittata","label":"Caltha sagittata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cambarus latimanus","label":"Cambarus latimanus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"candida albicans","label":"Candida albicans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"canis familiaris","label":"Canis familiaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cannabis sativa","label":"Cannabis sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caretta caretta","label":"Caretta caretta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cassiopea xamachana","label":"Cassiopea xamachana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caulobacter vibrioides","label":"Caulobacter vibrioides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cephalopods","label":"Cephalopoda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cerastium arvense","label":"Cerastium arvense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceriodaphnia","label":"Ceriodaphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceroglossus suturalis","label":"Ceroglossus suturalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chaetoceros","label":"Chaetoceros","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chamaecrista fasciculata","label":"Chamaecrista fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chilicola chalcidiformis","label":"Chilicola chalcidiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chitinimonas","label":"Chitinimonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chlamydomonas reinhardtii","label":"Chlamydomonas reinhardtii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chromobacterium","label":"Chromobacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysemys picta","label":"Chrysemys picta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysoperla rufilabris","label":"Chrysoperla rufilabris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"citrus","label":"Citrus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"clavibacter sp.","label":"Clavibacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"colinus virginianus","label":"Colinus virginianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crassostrea virginica","label":"Crassostrea virginica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crithidia fasciculata","label":"Crithidia fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cutibacterium acnes","label":"Cutibacterium acnes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cyanobacteria","label":"Cyanobacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia","label":"Daphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia pulex","label":"Daphnia pulex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera","label":"Diabrotica virgifera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera virgifera virus 1","label":"Diabrotica virgifera virgifera virus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"d. discoideum","label":"Dictyostelium discoideum","imageSrc":"dicty.png","imageAlt":"D. discoideum","mod":"dictyBase","modLink":"http://dictybase.org","linkVariable":""},{"value":"diptera","label":"Diptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dotocryptus bellicosus","label":"Dotocryptus bellicosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drechmeria coniospora","label":"Drechmeria coniospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drosophila","label":"Drosophila","imageSrc":"drosophila.png","imageAlt":"Drosophila graphic by Zoe Zorn CC BY 4.0","mod":"FlyBase","modLink":"https://flybase.org/doi/","linkVariable":"doi"},{"value":"dryopteris campyloptera","label":"Dryopteris campyloptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris expansa","label":"Dryopteris expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris intermedia","label":"Dryopteris intermedia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dugesia dorotocephala","label":"Dugesia dorotocephala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"elasmobranchii","label":"Elasmobranchii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"embryophyta","label":"Embryophyta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enoploteuthis chunii","label":"Enoploteuthis chunii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterobacter aerogenes","label":"Enterobacter aerogenes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterococcus raffinosus","label":"Enterococcus raffinosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"epichloë coenophiala","label":"Epichloë coenophiala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"equus caballus","label":"Equus caballus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erigeron sp","label":"Erigeron sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eristalis","label":"Eristalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eruca vesicaria","label":"Eruca vesicaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erwinia carotovora","label":"Erwinia carotovora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erythronium americanum","label":"Erythronium americanum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"escherichia coli","label":"Escherichia coli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eukaryota","label":"Eukaryotes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"felis catus","label":"Felis catus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella novicida","label":"Francisella novicida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella tularensis","label":"Francisella tularensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fraxinus americana","label":"Fraxinus americana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fucus distichus","label":"Fucus distichus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fungi","label":"Fungi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gasteropelecus sp.","label":"Gasteropelecus sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"geranium sp","label":"Geranium sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"girardia","label":"Girardia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glaucomys volans","label":"Glaucomys volans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glycine max","label":"Glycine max","imageSrc":"","imageAlt":"","mod":"Soybase","modLink":"https://soybase.org","linkVariable":""},{"value":"glyptemys insculpta","label":"Glyptemys insculpta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gossypium hirsutum","label":"Gossypium hirsutum","imageSrc":"","imageAlt":"","mod":"CottonGen","modLink":"https://www.cottongen.org/","linkVariable":""},{"value":"gromphadorhina portentosa","label":"Gromphadorhina portentosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gryllodes sigillatus","label":"Gryllodes sigillatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"haliotis rufescens","label":"Haliotis rufescens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hepacivirus hominis","label":"Hepatitis C Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"herpes simplex virus type 1","label":"Herpes simplex virus type 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human","label":"Human","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human coronavirus oc43","label":"Human coronavirus OC43","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydra vulgaris","label":"Hydra vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydropsyche sp","label":"Hydropsyche sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hymenoptera","label":"Hymenoptera","imageSrc":"","imageAlt":"","mod":"Hymenoptera Genome Database","modLink":"https://hymenoptera.elsiklab.missouri.edu/","linkVariable":""},{"value":"hypochaeris radicata","label":"Hypochaeris radicata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hypodynerus vespiformis","label":"Hypodynerus vespiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflaviridae","label":"Iflaviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflavuris","label":"Iflavirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ipomoea hederacea","label":"Ipomoea hederacea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera","label":"Ischnomera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera ruficollis","label":"Ischnomera ruficollis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"julidochromis marlieri","label":"Julidochromis marlieri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"juniperus virginiana","label":"Juniperus virginiana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"kluyveromyces marxianus","label":"Kluyveromyces marxianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"l. casei","label":"L. casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lacticaseibacillus casei","label":"Lacticaseibacillus casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"larentiinae sp","label":"Larentiinae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"laurus nobilis","label":"Laurus nobilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lepidoptera","label":"Lepidoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"leucanthemum vulgare","label":"Leucanthemum vulgare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"linepithema humile","label":"Linepithema humile","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"liometopum occidentale","label":"Liometopum occidentale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lolium arundinaceum","label":"Lolium arundinaceum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbriculus variegatus","label":"Lumbriculus variegatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbricus terrestris","label":"Lumbricus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lupinus polyphyllus","label":"Lupinus polyphyllus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lycorma delicatula","label":"Lycorma delicatula","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lynx rufus","label":"Lynx rufus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"magnaporthe oryzae","label":"Magnaporthe oryzae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mammalia","label":"Mammalia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"manihot esculenta","label":"Manihot esculenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"medicago lupulina","label":"Medicago lupulina","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"meloidogyne","label":"Meloidogyne","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mimus polyglottos","label":"Mimus polyglottos","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bryophyta","label":"Mosses","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mouse","label":"Mouse","imageSrc":"","imageAlt":"","mod":"MGI","modLink":"https://informatics.jax.org","linkVariable":""},{"value":"m. minutoides","label":"Mus minutoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mycobacterium smegmatis","label":"Mycobacterium smegmatis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nakaseomyces glabratus","label":"Nakaseomyces glabratus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nauphoeta cinerea","label":"Nauphoeta cinerea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"neurospora","label":"Neurospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"n. benthamiana","label":"Nicotiana benthamiana","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/Nicotiana_benthamiana/genome","linkVariable":""},{"value":"nicotiana tabacum","label":"Nicotiana tabacum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae","label":"Noctuidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae sp","label":"Noctuidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nothobranchius furzeri","label":"Nothobranchius furzeri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"onchocerca volvulus","label":"Onchocerca volvulus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"orconectes virilis","label":"Orconectes virilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ormia ochracea","label":"Ormia ochracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"o. sativa","label":"Oryza sativa","imageSrc":"","imageAlt":"","mod":"Gramene","modLink":"https://www.gramene.org/","linkVariable":""},{"value":"other","label":"Other","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"oxalis enneaphylla","label":"Oxalis enneaphylla","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea","label":"Pantoea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea agglomerans","label":"Pantoea agglomerans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"papaver sp","label":"Papaver sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paramecium bursaria","label":"Paramecium bursaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"partitiviridae","label":"Partitiviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pelodiscus sinensis","label":"Pelodiscus sinensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"perezia recurvata","label":"Perezia recurvata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"petromyzon marinus","label":"Petromyzon marinus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis","label":"Photinus pyralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis associated partiti-like virus","label":"Photinus pyralis associated partiti-like virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis iflavirus 1","label":"Photinus pyralis iflavirus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"physcomitrium patens","label":"Physcomitrium patens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus strobus","label":"Pinus strobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus taeda","label":"Pinus taeda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"platycheirus","label":"Platycheirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"plectus sambesii","label":"Plectus sambesii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pogonomyrmex occidentalis","label":"Pogonomyrmex occidentalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"poncirus trifoliata","label":"Poncirus trifoliata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"populus deltoides","label":"Populus deltoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"potato virus y","label":"Potato virus Y","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"primula magellanica","label":"Primula magellanica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pristionchus pacificus","label":"Pristionchus pacificus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"prunus persica","label":"Prunus persica","imageSrc":"","imageAlt":"","mod":"Genome Database for Rosaceae","modLink":"https://www.rosaceae.org/","linkVariable":""},{"value":"psalmopoeus iriminia","label":"Psalmopoeus iriminia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudanabaena sp.","label":"Pseudanabaena sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas","label":"Pseudomonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas aeruginosa","label":"Pseudomonas aeruginosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas glycinae","label":"Pseudomonas glycinae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas putida","label":"Pseudomonas putida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas syringae","label":"Pseudomonas syringae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pterophyllum scalare","label":"Pterophyllum scalare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"python regius","label":"Python regius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"quercus macrocarpa","label":"Quercus macrocarpa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ralstonia solanacearum","label":"Ralstonia solanacearum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranitomeya imitator","label":"Ranitomeya imitator","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranunculus peduncularis","label":"Ranunculus peduncularis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"rat","label":"Rat","imageSrc":"","imageAlt":"","mod":"RGD","modLink":"https://rgd.mcw.edu","linkVariable":""},{"value":"rheinheimera","label":"Rheinheimera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ribes rubrum","label":"Ribes rubrum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"sars-cov-2","label":"SARS-CoV-2","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. cerevisiae","label":"Saccharomyces cerevisiae","imageSrc":"yeast.png","imageAlt":"Yeast graphic by Zoe Zorn CC BY 4.0","mod":"SGD","modLink":"https://yeastgenome.org","linkVariable":""},{"value":"saccharomyces paradoxus","label":"Saccharomyces paradoxus ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. uvarum","label":"Saccharomyces uvarum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schistosoma","label":"Schistosoma","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schizosaccharomyces japonicus","label":"Schizosaccharomyces japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. pombe","label":"Schizosaccharomyces pombe","imageSrc":"pombe.png","imageAlt":"Pombe graphic by Zoe Zorn © Caltech","mod":"PomBase","modLink":"https://www.pombase.org/reference/PMID:","linkVariable":"pmId"},{"value":"schmidtea mediterranea","label":"Schmidtea mediterranea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"senecio sp","label":"Senecio sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"simocephalus","label":"Simocephalus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"siraitia grosvenorii","label":"Siraitia grosvenorii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"solanum lycopersicum","label":"Solanum lycopersicum","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/1/view/","linkVariable":""},{"value":"sorghum","label":"Sorghum","imageSrc":"","imageAlt":"","mod":"SorghumBase","modLink":"https://www.sorghumbase.org","linkVariable":""},{"value":"spiroplasma eriocheiris","label":"Spiroplasma eriocheiris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus aureus","label":"Staphylococcus aureus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus epidermidis","label":"Staphylococcus epidermidis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"steinernema carpocapsae","label":"Steinernema carpocapsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"steinernema hermaphroditum","label":"Steinernema hermaphroditum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stenotrophomonas geniculata","label":"Stenotrophomonas geniculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus gordonii ","label":"Streptococcus gordonii ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus mutans","label":"Streptococcus mutans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":" streptococcus pneumoniae","label":"Streptococcus pneumoniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. purpuratus","label":"Strongylocentrotus purpuratus","imageSrc":"","imageAlt":"","mod":"Echinobase","modLink":"https://www.echinobase.org","linkVariable":""},{"value":"strongyloides ratti","label":"Strongyloides ratti","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"sulfolobus","label":"Sulfolobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"symphoricarpos albus","label":"Symphoricarpos albus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syncirsodes","label":"Syncirsodes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"synechococcus elongatus","label":"Synechococcus elongatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syrphidae","label":"Syrphidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tarantobelus jeffdanielsi","label":"Tarantobelus jeffdanielsi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"taraxacum officinale","label":"Taraxacum officinale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tatochila theodice","label":"Tatochila theodice","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetrahymena","label":"Tetrahymena","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetramorium immigrans","label":"Tetramorium immigrans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tomato brown rugose fruit virus","label":"ToBRFV","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trachemys scripta","label":"Trachemys scripta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tribolium castaneum","label":"Tribolium castaneum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichoptera","label":"Trichoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichuris muris","label":"Trichuris muris","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"trifolium repens","label":"Trifolium repens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trypoxylus dichotomus","label":"Trypoxylus dichotomus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tsuga canadensis","label":"Tsuga canadensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ulva expansa","label":"Ulva expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"universal","label":"Universal","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"vargula hilgendorfii","label":"Vargula hilgendorfii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"vespula vulgaris","label":"Vespula vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"virus","label":"Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"watasenia scintillans","label":"Watasenia scintillans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"wolbachia pipientis","label":"Wolbachia pipientis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"xenopus","label":"Xenopus","imageSrc":"xenopus.png","imageAlt":"Xenopus graphic by Zoe Zorn CC BY 4.0","mod":"XenBase","modLink":"https://xenbase.org","linkVariable":""},{"value":"xenorhabdus griffiniae","label":"Xenorhabdus griffiniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"yramea cytheris","label":"Yramea cytheris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zaprionus indianus","label":"Zaprionus indianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zea mays","label":"Zea mays","imageSrc":"","imageAlt":"","mod":"MaizeDB","modLink":"","linkVariable":""},{"value":"zebrafish","label":"Zebrafish","imageSrc":"zebrafish.png","imageAlt":"Zebrafish graphic by Zoe Zorn CC BY 4.0","mod":"ZFIN","modLink":"https://zfin.org","linkVariable":""}]}},"pageContext":{"id":"b810f3f2-a55e-4958-a1ce-2db0c527bf66","citedBy":[],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}