vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

PeerJ

Volumn 2017, Issue 5, 2017, Pages

  Bolduc, Benjamin ^a   Jang, Ho Bin ^a   Doulcier, Guilhem ^b,c   You, Zhi Qiang ^a   Roux, Simon ^a   Sullivan, Matthew B ^a,d  

^a OHIO STATE UNIVERSITY   (United States)

^b PSL RESEARCH UNIVERSITY   (France)

^c PSL RESEARCH UNIVERSITY   (France)

^d The Ohio State University   (United States)

Author keywords

Archaeal viruses; Bacteriophage; Taxonomy; Virus

Indexed keywords

ARCHAEAL VIRUS; ARCHAEON; CASE REPORT; DOUBLE-STRANDED DNA VIRUS; GENE TRANSFER; HUMAN; NONHUMAN; PROTEIN CONTENT; SCIENTIST; TAXONOMY; VIRUS GENOME;

EID: 85018974675     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.3243     Document Type: Article

References (63)

1. Abbasifar R, Kropinski AM, Sabour PM, Ackermann H-W, Alanis Villa A, Abbasifar A, Griffiths MW. 2013. The genome of Cronobacter sakazakii bacteriophage vB_CsaP_GAP227 suggests a new genus within the Autographivirinae. Genome Announcements 1:e00122-12-e00122-12 DOI 10.1128/genomeA.00122-12
2. Ågren J, Sundström A, Håfström T, Segerman B. 2012. Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLOS ONE 7:e39107 DOI 10.1371/journal.pone.0039107
3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389-3402
4. Assenov Y, Ramirez F, Schelhorn S-E, Lengauer T, Albrecht M. 2008. Computing topological parameters of biological networks. Bioinformatics 24:282-284 DOI 10.1093/bioinformatics/btm554
5. Barberán A, Bates ST, Casamayor EO, Fierer N. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. The ISME Journal 6:343-351
6. Bergsten J. 2005. A review of long-branch attraction. Cladistics 21:163-193 DOI 10.1111/j.1096-0031.2005.00059.x
7. Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB. 2016. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal 11:7-14 DOI 10.1038/ismej.2016.89
8. Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, De Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB. 2015. Patterns and ecological drivers of ocean viral communities. Science 348:1261498-1261498 DOI 10.1126/science.1261498
9. Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. 2016. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environmental Microbiology 18:1162-1175 DOI 10.1111/1462-2920.13127
10. Comeau AM, Krisch HM. 2008. The capsid of the T4 phage superfamily: the evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Molecular Biology and Evolution 25:1321-1332 DOI 10.1093/molbev/msn080
11. Corel E, Lopez P, Méheust R, Bapteste E. 2016. Network-thinking: graphs to analyze microbial complexity and evolution. Trends in Microbiology 24:224-227 DOI 10.1016/j.tim.2015.12.003
12. Dagan T. 2011. Phylogenomic networks. Trends in Microbiology 19:483-491 DOI 10.1016/j.tim.2011.07.001
13. Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB. 2014. Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513:242-245 DOI 10.1038/nature13459
14. Edwards RA, Rohwer F. 2002. The phage proteomic tree: a genome-based taxonomy for phage. Journal of Bacteriology 184:4529-4535 DOI 10.1128/JB.184.16.4529-4535.2002
15. Edwards RA, Rohwer F. 2005. Viral metagenomics. Nature Reviews Microbiology 3:504-510 DOI 10.1038/nrmicro1163
16. Eriksson H, Maciejewska B, Latka A, Majkowska-Skrobek G, Hellstr M, Melefors ö, Wang JT, Kropinski AM, Drulis-Kawa Z, Nilsson AS. 2015. A suggested new bacteriophage genus, ''Kp34likevirus'', within the Autographivirinae subfamily of podoviridae. Viruses 7:1804-1822 DOI 10.3390/v7041804
17. Fauquet CM, Fargette D. 2005. International committee on taxonomy of viruses and the 3,142 unassigned species. Virology Journal 2:1-10 DOI 10.1186/1743-422X-2-64
18. Filee J. 2006. A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Molecular Biology and Evolution 23:1688-1696 DOI 10.1093/molbev/msl036
19. Fortunato S. 2010. Community detection in graphs. Physics and Reports 486:75-174 DOI 10.1016/j.physrep.2009.11.002
20. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S-J, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D. 2011. The iPlant collaborative: cyberinfrastructure for plant biology. Frontiers in Plant Science 2:1-16 DOI 10.3389/fpls.2011.00034
21. Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, Forterre P, Campanacci V, Cambillau C. 2009. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proceedings of the National Academy of Sciences of the United States of America 106:21155-21160 DOI 10.1073/pnas.0909893106
22. Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copel A, Sudek S, Maitl A, Chittick L, Dos Santos F, Weitz JS, Worden AZ, Woyke T, Sullivan MB. 2016. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17:930 DOI 10.1186/s12864-016-3286-x
23. Grose JH, Casjens SR. 2014. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468:421-443 DOI 10.1016/j.virol.2014.08.024
24. Gutiérrez D, Adriaenssens EM, Martínez B, Rodríguez A, Lavigne R, Kropinski AM, García P. 2014. Three proposed new bacteriophage genera of staphylococcal phages: ''3alikevirus'', ''77likevirus'' and ''Phietalikevirus''. Archieves of Virology 159:389-398 DOI 10.1007/s00705-013-1833-1
25. Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E. 2009. Network analyses structure genetic diversity in independent genetic worlds. Proceedings of the National Academy of Sciences of the United States of America 107:127-132 DOI 10.1073/pnas.0908978107
26. Huang G, Le S, Peng Y, Zhao Y, Yin S, Zhang L, Yao X, Tan Y, Li M, Hu F. 2013. Characterization and genome sequencing of phage Abp1, a new phiKMV-like virus infecting multidrug-resistant acinetobacter baumannii. Current Microbiology 66:535-543 DOI 10.1007/s00284-013-0308-7
27. Hurwitz BL, Brum JR, Sullivan MB. 2014. Depth-stratified functional and taxonomic niche specialization in the ''core'' and ''flexible'' Pacific Ocean Virome. The ISME Journal 9:1-13 DOI 10.1038/ismej.2014.143
28. Hurwitz BL, Hallam SJ, Sullivan MB. 2013. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biology 14:1-14 DOI 10.1186/gb-2013-14-11-r123
29. Iranzo J, Koonin EV, Prangishvili D, Krupovic M. 2016. Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements. Journal of Virology 90:11043-11055 DOI 10.1128/JVI.01622-16
30. Iranzo J, Krupovic M, Koonin EV. 2016. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. mBio 7:e00978-16 DOI 10.1128/mBio.00978-16
31. Jang HB, Fagutao FF, Nho SW, Park SB, Cha IS, Yu JE, Lee JS, Im SP, Aoki T, Jung TS. 2013. Phylogenomic network and comparative genomics reveal a diverged member of the 8KZ-related group, marine vibrio phage 8JM-2012. Journal of Virology 87:12866-12878 DOI 10.1128/JVI.02656-13
32. Keen EC, Bliskovsky VV, Malagon F, Baker JD, Prince JS, Klaus JS, Adhya SL. 2017. Novel ''Superspreader'' bacteriophages promote horizontal gene transfer by transformation. mBio 8:1-12 DOI 10.1128/mBio.02115-16
33. Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MRC, Barylski J, Ackermann H-W, Kuhn JH. 2016. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology 161:1095-1099 DOI 10.1007/s00705-015-2728-0
34. Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Eric Wommack K, Stepanauskas R. 2015. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. The ISME Journal 9:2386-2399 DOI 10.1038/ismej.2015.48
35. Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW. 2013. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology 15:1356-1376 DOI 10.1111/1462-2920.12053
36. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM. 2009. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiology 9:224 DOI 10.1186/1471-2180-9-224
37. Lawrence JG, Hatfull GF, Hendrix RW. 2002. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Journal of Bacteriology 184:4891-4905 DOI 10.1128/JB.184.17.4891-4905.2002
38. Leplae R, Hebrant A, Wodak SJ, Toussaint A. 2004. ACLAME: a Classification of Mobile genetic Elements. Nucleic Acids Research 32:D45-D49 DOI 10.1093/nar/gkh084
39. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. 2008. Reticulate representation of evolutionary and functional relationships between phage genomes. Molecular Biology and Evolution 25:762-777 DOI 10.1093/molbev/msn023
40. Manrique P, Bolduc B, Walk ST, Van der Oost J, Young MJ. 2016. Healthy human gut phageome. Proceedings of the National Academy of Sciences of the United States of America 113:10400-10405 DOI 10.1073/pnas.1601060113
41. Marston MF, Amrich CG. 2009. Recombination and microdiversity in coastal marine cyanophages. Environmental Microbiology 11:2893-2903 DOI 10.1111/j.1462-2920.2009.02037.x
42. Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ. 2009. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environmental Microbiology 11:2370-2387 DOI 10.1111/j.1462-2920.2009.01966.x
43. Nepusz T, Yu H, Paccanaro A. 2012. Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods 9:471-472 DOI 10.1038/nmeth.1938
44. Niu YD, McAllister TA, Nash JHE, Kropinski AM, Stanford K. 2014. Four Escherichia coli O157:H7 phages: a new bacteriophage genus and taxonomic classification of T1-like phages. PLOS ONE 9:e100426 DOI 10.1371/journal.pone.0100426
45. Norman JM, Handley S, Baldridge M, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DPB, Keshavarzian A, Mutlu EA, Sauk J, Xavier RJ, Wang D, Parkes M, Virgin H. 2015. Disease-specific alternations in the enteric virome in inflammatory bowel disease. Cell 160:447-460 DOI 10.1016/j.cell.2015.01.002
46. Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, Reddy TBK, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC. 2017. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Research 45:D457-D465 DOI 10.1093/nar/gkw1030
47. Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. 2016. Uncovering Earth's virome. Nature 536:425-430 DOI 10.1038/nature19094
48. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 4:e06416 DOI 10.7554/eLife.06416
49. Prangishvili D, Garrett RA, Koonin EV. 2006. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Research 117:52-67
50. Prangishvili D, Krupovič M. 2012. A new proposed taxon for double-stranded DNA viruses, the order ''Ligamenvirales''. Archives of Virology 157:791-795 DOI 10.1007/s00705-012-1229-7
51. Redder P, Peng X, Brugger K, Shah SA, Roesch F, Greve B, She Q, Schleper C, Forterre P, Garrett RA, Prangishvili D. 2009. Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environmental Microbiology 11:2849-2862
52. Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Bork P, Acinas SG, Wincker P, Sullivan MB. 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537:689-693 DOI 10.1038/nature19366
53. Roux S, Enault F, Ravet V, Pereira O, Sullivan MB. 2015. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Frontiers in Microbiology 6:199 DOI 10.3389/fmicb.2015.00199
54. Roux S, Hallam SJ, Woyke T, Sullivan MB. 2015. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife 4:e08490 DOI 10.7554/eLife.08490
55. Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. 2014. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell-and meta-genomics. eLife 3:e03125 DOI 10.7554/eLife.03125
56. Schaeffer SE. 2007. Graph clustering. Computer Science Review 1:27-64 DOI 10.1016/j.cosrev.2007.05.001
57. Shih YK, Parthasarathy S. 2012. Identifying functional modules in interaction networks through overlapping Markov clustering. Bioinformatics 28:i473-i479 DOI 10.1093/bioinformatics/bts370
58. Simmonds P. 2015. Methods for virus classification and the challenge of incorporating metagenomic sequence data. Journal of General Virology 96:1193-1206 DOI 10.1099/vir.0.000016
59. Simmonds P, Adams MJ, Benkö M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hul R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, Van der Vlugt RA, Varsan A, Zerbin FM. 2017. Consensus statement: virus taxonomy in the age of metagenomics. Nature Reviews 15:161-168 DOI 10.1038/nrmicro.2016.177
60. Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLOS Biology 4:1344-1357 DOI 10.1371/journal.pbio.0040234
61. Wittmann J, Klumpp J, Moreno Switt AI, Yagubi A, Ackermann HW, Wied-mann M, Svircev A, Nash JH, Kropinski AM. 2015. Taxonomic reassessment of N4-like viruses using comparative genomics and proteomics suggests a new subfamily-''Enquartavirinae''. Archives of Virology 160:3053-3062 DOI 10.1007/s00705-015-2609-6
62. Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America 87:4576-4579
63. Zanotto PM, Gibbs MJ, Gould EA, Holmes EC. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. Journal of Virology 70:6083-6096