Four novel algal virus genomes discovered from Yellowstone Lake metagenomes

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Zhang, Weijia ^a   Zhou, Jinglie ^a,b   Liu, Taigang ^a   Yu, Yongxin ^a,c   Pan, Yingjie ^a,c   Yan, Shuling ^a,d   Wang, Yongjie ^a,c  

^a SHANGHAI OCEAN UNIVERSITY   (China)

^b AUBURN UNIVERSITY   (United States)

^c AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

^d UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENE ORDER; GENETIC VARIATION; GENETICS; LAKE; METAGENOME; METAGENOMICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; OPEN READING FRAME; PHYCODNAVIRIDAE; PHYLOGENY; PROCEDURES; VIROLOGY; VIRUS GENOME;

EVOLUTION, MOLECULAR; GENE ORDER; GENETIC VARIATION; GENOME, VIRAL; LAKES; METAGENOME; METAGENOMICS; MULTIGENE FAMILY; OPEN READING FRAMES; PHYCODNAVIRIDAE; PHYLOGENY;

EID: 84944144935     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep15131     Document Type: Article

References (34)

1. Wilson, W. H., Van Etten, J. L., Allen, M. J. The Phycodnaviridae: the story of how tiny giants rule the world. Curr Top Microbiol Immunol 328, 1-42 (2009).
2. Suttle, C. A. Viruses in the sea. Nature 437, 356-361 (2005).
3. International Committee on Taxonomy of Viruses. In Virus Taxonomy: Classification and Nomenclature of Viruses:NINTH REPORT OF THE INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUSES (eds King, A. et al.), 249-262 (2012).
4. Dunigan, D. D., Fitzgerald, L. A., Van Etten, J. L. Phycodnaviruses: a peek at genetic diversity. Virus Res 117, 119-132 (2006).
5. Derelle, E. et al. Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS One 3, e2250 (2008).
6. Weynberg, K. D., Allen, M. J., Ashelford, K., Scanlan, D. J., Wilson, W. H. From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV-1. Environ Microbiol 11, 2821-2839 (2009).
7. Moreau, H. et al. Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer. J Virol 84, 12555-12563 (2010).
8. Fitzgerald, L. A. et al. Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi. Virology 358, 459-471 (2007).
9. Fitzgerald, L. A. et al. Sequence and annotation of the 369-kb NY-2 A and the 345-kb AR158 viruses that infect Chlorella NC64A. Virology 358, 472-484 (2007).
10. Fitzgerald, L. A. et al. Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon Acanthocystis turfacea. Virology 362, 350-361 (2007).
11. Iyer, L. M., Balaji, S., Koonin, E. V., Aravind, L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117, 156-184 (2006).
12. Colson, P., de Lamballerie, X., Fournous, G., Raoult, D. Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales. Intervirology 55, 321-332 (2012).
13. Yutin, N., Wolf, Y. I., Raoult, D., Koonin, E. V. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J 6, 223 (2009).
14. La Scola, B. et al. The virophage as a unique parasite of the giant mimivirus. Nature 455, 100-104 (2008).
15. Zhou, J. et al. Diversity of virophages in metagenomic data sets. J Virol 87, 4225-4236 (2013).
16. Zhou, J. et al. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. J Virol 89, 1278-1285 (2015).
17. Clingenpeel, S. et al. Yellowstone Lake: high-energy geochemistry and rich bacterial diversity. Environ Microbiol 13, 2172-2185 (2011).
18. Yau, S. et al. Virophage control of antarctic algal host-virus dynamics. PNAS 108, 6163-6168 (2011).
19. Huang, Y., Niu, B., Gao, Y., Fu, L., Li, W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26, 680-682 (2010).
20. Marchler-Bauer, A. et al. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41, D348-352 (2013).
21. Tatusov, R. L. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22-28 (2001).
22. Darling, A. C., Mau, B., Blattner, F. R., Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394-1403 (2004).
23. Xu, Z., Wang, H. LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35, W265-268 (2007).
24. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797 (2004).
25. Santini, S. et al. Genome of Phaeocystis globosa virus PgV-16 T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. PNAS 110, 10800-10805 (2013).
26. Ninio, S., Elbaz, Y., Schuldiner, S. The membrane topology of EmrE-a small multidrug transporter from Escherichia coli. FEBS Lett 562, 193-196 (2004).
27. Yutin, N., Colson, P., Raoult, D., Koonin, E. V. Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. Virol J 10, 106 (2013).
28. Yutin, N., Wolf, Y. I., Koonin, E. V. Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology, 38-52 (2014).
29. Lovalvo, D. et al. A geothermal-linked biological oasis in Yellowstone Lake, Yellowstone National Park, Wyoming. Geobiology 8, 327-336 (2010).
30. Gaia, M. et al. Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter. PLoS One 8, e61912 (2013).
31. Fischer, M. G., Suttle, C. A. A virophage at the origin of large DNA transposons. Science 332, 231-234 (2011).
32. Gaia, M. et al. Zamilon, a novel virophage with Mimiviridae host specificity. PLoS One 9, e94923 (2014).
33. Krupovic, M., Bamford, D. H., Koonin, E. V. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol Direct 9, 6 (2014).
34. Claverie, J. M. Giant virus in the sea: Extending the realm of Megaviridae to Viridiplantae. Commun Integr Biol 6, e25685 (2013).