Novel phycodnavirus genes amplified from Canadian freshwater environments

Aquatic Microbial Ecology

Volumn 63, Issue 1, 2011, Pages 61-67

  Short, Steven M ^a   Rusanova, Oksana ^a   Staniewski, Michael A ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Algal viruses; Chlorella viruses; DNA polymerase; Freshwater; Phycodnaviruses; PolB; Prymnesioviruses

Indexed keywords

ALGAE; CHLORELLA VIRUS; CHLOROPHYTA; CHLOROVIRUS; PHYCODNAVIRIDAE;

EID: 79956295882     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01478     Document Type: Article

References (25)

1. Bellec L, Grimsley N, Moreau H, Desdevises Y (2009) Phylogenetic analysis of new prasinoviruses (Phycodnaviridae) that infect the green unicellular algae Ostreococcus, Bathycoccus and Micromonas. Environ Microbiol Rep 1: 114-123
2. Brussaard CPD, Short SM, Frederickson CM, Suttle CA (2004) Isolation and phylogenetic analysis of novel viruses infecting the phytoplankton Phaeocystis globosa (Prymnesiophyceae). Appl Environ Microbiol 70:3700-3705 (Pubitemid 38745920)
3. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552 (Pubitemid 30210700)
4. Chen F, Suttle CA (1995) Amplification of DNA-polymerase gene fragments from viruses infecting microalgae. Appl Environ Microbiol 61:1274-1278
5. Chen F, Suttle CA, Short SM (1996) Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl Environ Microbiol 62:2869-2874 (Pubitemid 26260093)
6. Clasen JL, Suttle CA (2009) Identification of freshwater Phycodnaviridae and their potential phytoplankton hosts, using DNA pol sequence fragments and a genetic-distance analysis. Appl Environ Microbiol 75:991-997
7. Culley AI, Asuncion BF, Steward GF (2009) Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae. ISME J 3: 409-418
8. Dereeper A, Guignon V, Blanc G, Audic S and others (2008) Phylogeny.fr: robust phylogenetic analysis for the nonspecialist. Nucleic Acids Res 36:W465-W469
9. Dunigan DD, Fitzgerald LA, Van Etten JL (2006) Phycodnaviruses: a peek at genetic diversity. Virus Res 117: 119-132
10. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797 (Pubitemid 38832724)
11. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704 (Pubitemid 37365050)
12. Iyer LM, Balaji S, Koonin EV, Aravind L (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117:156-184
13. Larsen JB, Larsen A, Bratbak G, Sandaa RA (2008) Phylogenetic analysis of members of the Phycodnaviridae virus family using amplified fragments of the major capsid protein gene. Appl Environ Microbiol 74:3048-3057 (Pubitemid 351747009)
14. Lawrence JE, Steward GF (2010) Purification of viruses by centrifugation. In: Wilhelm SW, Weinbauer MG, Suttle CA (eds) Manual of aquatic viral ecology. American Society of Limnology and Oceanography, Waco, TX, p 166-181
15. Markine-Goriaynoff N, Gillet L, Van Etten JL, Korres H, Verma N, Vanderplasschen A (2004) Glycosyltransferases encoded by viruses. J Gen Virol 85:2741-2754 (Pubitemid 39360017)
16. Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H (2008) Marine mimivirus relatives are probably large algal viruses. Virol J 5:12
17. Munawar M, Munawar IF (1996) Phytoplankton dynamics in the North American great lakes, Vol 1: Lake Ontario, Erie and St. Clair. SPB Academic Publishing, Amsterdam
18. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574 (Pubitemid 37038874)
19. Short CM, Rusanova O, Short SM (in press) Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada. ISME J doi:10.1038/ismej.2010.183
20. Short SM, Short CM (2008) Diversity of algal viruses in various North American freshwater environments. Aquat Microb Ecol 51:13-21 (Pubitemid 351785224)
21. Short SM, Suttle CA (2002) Sequence analysis of marine virus communities reveals that groups of related algal viruses are widely distributed in nature. Appl Environ Microbiol 68:1290-1296 (Pubitemid 34205368)
22. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
23. Vardi A, Van Mooy BAS, Fredricks HF, Popendorf KJ, Ossolinski JE, Haramaty L, Bidle KD (2009) Viral glycosphingolipids induce lytic infection and cell death in marine phytoplankton. Science 326:861-865
24. Wilson WH, Schroeder DC, Allen MJ, Holden MTG and others (2005) Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 309: 1090-1092 (Pubitemid 41134469)
25. Wommack KE, Sime-Ngando T, Winget DM, Jamindar S, Helton RR (2010) Filtration-based methods for the collection of viral concentrates from large water samples. In: Wilhelm SW, Weinbauer MG, Suttle CA (eds) Manual of aquatic viral ecology. American Society of Limnology and Oceanography, Waco, TX, p 110-117