Draft genome sequence of the coccolithovirus EhV-84

Wilson WH, Schroeder DC, Allen MJ, Holden MTG, Parkhill J, Barrell BG, Churcher C, Harnlin N, Mungall K, Norbertczak H, et al. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 2005; 309:1090–1092. PubMed doi:10.1126/science.1113109 Coyle KO, Pinchuk AI. Climate-related differences in zooplankton density and growth on the inner shelf of the southeastern Bering Sea. Prog Oceanogr 2002; 55:177–194. doi:10.1016/S0079-6611(02)00077-0 Brown CW, Yoder JA. Coccolithophorid Blooms in the Global Ocean. Journal of Geophysical Research-Oceans 1994; 99(C4):7467–7482. doi:10.1029/93JC02156 Holligan PM, Viollier M, Harbour DS, Camus P, Champagnephilippe M. Satellite and Ship Studies of Coccolithophore Production Along a Continental-Shelf Edge. Nature 1983; 304:339–342. doi:10.1038/304339a0 Holligan PM, Fernandez E, Aiken J, Balch WM, Boyd P, Burkill PH, Finch M, Groom SB, Malin G, Muller K, et al. A Biogeochemical Study of the Coccolithophore, Emiliania huxleyi, in the North-Atlantic. Global Biogeochem Cycles 1993; 7:879–900. doi:10.1029/93GB01731 Westbroek P, Brown CW, Vanbleijswijk J, Brownlee C, Brummer GJ, Conte M, Egge J, Fernandez E, Jordan R, Knappertsbusch M, et al. A Model System Approach to Biological Climate Forcing — the Example of Emiliania huxleyi. Global Planet Change 1993; 8:27–46. doi:10.1016/0921-8181(93)90061-R Schroeder DC, Oke J, Malin G, Wilson WH. Coccolithovirus (Phycodnaviridae): Characterisation of a new large dsDNA algal virus that infects Emiliania huxleyi. Arch Virol 2002; 147:1685–1698. PubMed doi:10.1007/s00705-002-0841-3 Allen MJ, Schroeder DC, Donkin A, Crawfurd KJ, Wilson WH. Genome comparison of two Coccolithoviruses. Virol J 2006; 3:15. PubMed doi:10.1186/1743-422X-3-15 Saitou N, Nei M. The Neighbor-Joining Method — a New Method for Reconstructing Phylogenetic Trees. Mol Biol Evol 1987; 4:406–425. PubMed Felsenstein J. Confidence-Limits on Phylogenies — an Approach Using the Bootstrap. Evolution 1985; 39:783–791. doi:10.2307/2408678 Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004; 101:11030–11035. PubMed doi:10.1073/pnas.0404206101 Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596–1599. PubMed doi:10.1093/molbev/msm092 Wilson WH, Tarran GA, Schroeder D, Cox M, Oke J, Malin G. Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel. J Mar Biol Assoc U K 2002; 82:369–377. doi:10.1017/S002531540200560X Wilson WH, Van Etten JL, Allen MJ. The Phycodnaviridae: The Story of How Tiny Giants Rule the World. Lesser Known Large Dsdna Viruses 2009; 328:1–42. PubMed doi:10.1007/978-3-540-68618-7_1 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556 Allen MJ, Martinez-Martinez J, Schroeder DC, Somerfield PJ, Wilson WH. Use of microarrays to assess viral diversity: from genotype to phenotype. Environ Microbiol 2007; 9:971–982. PubMed doi:10.1111/j.1462-2920.2006.01219.x Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556 Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie JM, Ogata H. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res 2009; 19:1441–1449. PubMed doi:10.1101/gr.091686.109 Michaelson LV, Dunn TM, Napier JA. Viral transdominant manipulation of algal sphingolipids. Trends Plant Sci 2010; 15:651–655. PubMed doi:10.1016/j.tplants.2010.09.004 Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng QD, Weiand M, et al. Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes. PLoS ONE 2010; 5:e9083. PubMed doi:10.1371/journal.pone.0009083 Allen MJ, Howard JA, Lilley KS, Wilson WH. Proteomic analysis of the EhV-86 virion. Proteome Sci 2008;6:11. PubMed doi:10.1186/1477-5956-6-11 The Broad Institute. Marine phage sequencing project protocols. http://www.broadinstitute.org/annotation/viral/Phage/Protocols.html Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393 Pagarete A, Allen MJ, Wilson WH, Kimmance SA, de Vargas C. Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: survival of the fattest. Environ Microbiol 2009; 11:2840–2848. PubMed doi:10.1111/j.1462-2920.2009.02006.x Allen MJ, Forster T, Schroeder DC, Hall M, Roy D, Ghazal P, Wilson WH. Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol 2006; 80:7699–7705. PubMed doi:10.1128/JVI.00491-06 Han G, Gable K, Yan LY, Allen MJ, Wilson WH, Moitra P, Harmon JM, Dunn TM. Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. J Biol Chem 2006; 281:39935–39942. PubMed doi:10.1074/jbc.M609365200 Schroeder DC, Oke J, Hall M, Malin G, Wilson WH. Virus succession observed during an Emiliania huxleyi bloom. Appl Environ Microbiol 2003; 69:2484–2490. PubMed doi:10.1128/AEM.69.5.2484-2490.2003 Martínez JM, Schroeder DC, Larsen A, Bratbak G, Wilson WH. Molecular dynamics of Emiliania huxleyi and cooccurring viruses during two separate mesocosm studies. Appl Environ Microbiol 2007; 73:554–562. PubMed doi:10.1128/AEM.00864-06 Iyer LM, Balaji S, Koonin EV, Aravind L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 2006; 117:156–184. PubMed doi:10.1016/j.virusres.2006.01.009