Mc Grath S, VanSinderen D: Bacteriophage: Genetics and molecular biology. 2007, Nortfolk, UK: Caister Academic Press
Google Scholar
Weinbauer MG, Rassoulzadegan F: Are viruses driving microbial diversification and diversity?. Environ Microbiol. 2004, 6: 1-11.
PubMed
Google Scholar
Wommack KE, Colwell RR: Virioplankton: Viruses in aquatic ecosystems. Microbiol Mol Biol R. 2000, 64: 69-114. 10.1128/MMBR.64.1.69-114.2000.
CAS
Google Scholar
Chen F, Lu JR: Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl Environ Microbiol. 2002, 68: 2589-2594. 10.1128/AEM.68.5.2589-2594.2002.
CAS
PubMed Central
PubMed
Google Scholar
Chenard C, Suttle CA: Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters. Appl Environ Microbiol. 2008, 74: 5317-5324. 10.1128/AEM.02480-07.
CAS
PubMed Central
PubMed
Google Scholar
Goldsmith DB, Crosti G, Dwivedi B, McDaniel LD, Varsani A, Suttle CA, Weinbauer MG, Sandaa RA, Breitbart M: Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microbiol. 2011, 77: 7730-7739. 10.1128/AEM.05531-11.
CAS
PubMed Central
PubMed
Google Scholar
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW: Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 2005, 438: 86-89. 10.1038/nature04111.
CAS
PubMed
Google Scholar
Mann NH, Clokie MRJ, Millard A, Cook A, Wilson WH, Wheatley PJ, Letarov A, Krisch HM: The genome of S-PM2, a “photosynthetic” T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol. 2005, 187: 3188-3200. 10.1128/JB.187.9.3188-3200.2005.
CAS
PubMed Central
PubMed
Google Scholar
Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ: Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ Microbiol. 2009, 11: 2370-2387. 10.1111/j.1462-2920.2009.01966.x.
CAS
PubMed
Google Scholar
Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W: Bacteriophage T4 genome. Microbiol Mol Biol R. 2003, 67: 86-156. 10.1128/MMBR.67.1.86-156.2003.
CAS
Google Scholar
Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, Jiang W, Chiu W, Hatfull GF, Hendrix RW, King J: Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: A “horned” bacteriophage of marine Synechococcus. J Biol Evol. 2007, 368: 966-981.
CAS
Google Scholar
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW: Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biol. 2005, 3: 790-806.
CAS
Google Scholar
Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, Chisholm SW: The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’. Environ Microbiol. 2009, 11: 2935-2951. 10.1111/j.1462-2920.2009.02081.x.
CAS
PubMed Central
PubMed
Google Scholar
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW: Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. 2006, 4: 1344-1357.
CAS
Google Scholar
Thompson LR: Auxiliary metabolic genes in viruses infecting marine cyanobacteria, Ph.D. thesis. 2010, Cambridge, MA: Massachusetts Institute of Technology
Google Scholar
Weigele PR, Pope WH, Pedulla ML, Houtz JM, Smith AL, Conway JF, King J, Hatfull GF, Lawrence JG, Hendrix RW: Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ Microbiol. 2007, 9: 1675-1695. 10.1111/j.1462-2920.2007.01285.x.
CAS
PubMed
Google Scholar
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW: Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 2007, 449: 83-86. 10.1038/nature06130.
CAS
PubMed
Google Scholar
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW: Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. PNAS. 2011, 108: E757-E764. 10.1073/pnas.1102164108.
CAS
PubMed Central
PubMed
Google Scholar
Jordan A, Reichard P: Ribonucleotide reductases. Annu Rev Biochem. 1998, 67: 71-98. 10.1146/annurev.biochem.67.1.71.
CAS
PubMed
Google Scholar
Lundin D, Torrents E, Poole AM, Sjoberg BM: RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics. 2009, 10: 589-597. 10.1186/1471-2164-10-589.
PubMed Central
PubMed
Google Scholar
Nordlund N, Reichard P: Ribonucleotide reductases. Annu Rev Biochem. 2006, 75: 681-706. 10.1146/annurev.biochem.75.103004.142443.
CAS
PubMed
Google Scholar
Hogbom M, Stenmark P, Voevodskaya N, McClarty G, Graslund A, Nordlund P: The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass. Science. 2004, 305: 245-248. 10.1126/science.1098419.
PubMed
Google Scholar
Lundin D, Gribaldo S, Torrents E, Sjoberg BM, Poole AM: Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evol Biol. 2010, 10: 383-402. 10.1186/1471-2148-10-383.
CAS
PubMed Central
PubMed
Google Scholar
Huang SJ, Wang K, Jiao NZ, Chen F: Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ Microbiol. 2012, 14: 540-558. 10.1111/j.1462-2920.2011.02667.x.
CAS
PubMed
Google Scholar
Lohr JE, Chen F, Hill RT: Genomic analysis of bacteriophage Phi JL001: Insights into its interaction with a sponge-associated alpha-proteobacterium. Appl Environ Microbiol. 2005, 71: 1598-1609. 10.1128/AEM.71.3.1598-1609.2005.
CAS
PubMed Central
PubMed
Google Scholar
Madigan MT, Martinko JM, Parker J: Brock Biology of Microorgranisms. 2003, Upper Saddle River, New Jersey: Prentice Hall, 10
Google Scholar
Rohwer F, Segall A, Steward G, Seguritan V, Breitbart M, Wolven F, Azam F: The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages. Limnol Oceanogr. 2000, 45: 408-418. 10.4319/lo.2000.45.2.0408.
CAS
Google Scholar
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F: The marine viromes of four oceanic regions. PLoS Biol. 2006, 4: 2121-2131.
CAS
Google Scholar
Aziz RK, Breitbart M, Edwards RA: Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 2010, 38: 4207-4217. 10.1093/nar/gkq140.
CAS
PubMed Central
PubMed
Google Scholar
Torrents E, Aloy P, Gibert I, Rodriguez-Trelles F: Ribonucleotide reductases: Divergent evolution of an ancient enzyme. J Mol Evol. 2002, 55: 138-152. 10.1007/s00239-002-2311-7.
CAS
PubMed
Google Scholar
Zhao YL, Wang K, Jiao NZ, Chen F: Genome sequences of two novel phages infecting marine roseobacters. Environ Microbiol. 2009, 11: 2055-2064. 10.1111/j.1462-2920.2009.01927.x.
CAS
PubMed Central
PubMed
Google Scholar
Matsuzaki S, Tanaka S, Koga T, Kawata T: A broad-host-range vibriophage, KVP40, isolated from sea-water. Microbiol Immunol. 1992, 36: 93-97.
CAS
PubMed
Google Scholar
Jordan A, Aslund F, Pontis E, Reichard P, Holmgren A: Characterization of Escherichia coli NrdH - A glutaredoxin-like protein with a thioredoxin-like activity profile. J Biol Chem. 1997, 272: 18044-18050. 10.1074/jbc.272.29.18044.
CAS
PubMed
Google Scholar
Stehr M, Schneider G, Aslund F, Holmgren A, Lindqvist Y: Structural basis for the thioredoxin-like activity profile of the glutaredoxin-like NrdH-redoxin from Escherichia coli. J Biol Chem. 2001, 276: 35836-35841. 10.1074/jbc.M105094200.
CAS
PubMed
Google Scholar
Andersson KK: Molecular anatomy and physiology of proteins: ribonucleotide reductase. 2008, New York: Nova Science Publishers, Inc
Google Scholar
Torrents E, Roca I, Gibert I: Corynebacterium ammoniagenes class Ib ribonucleotide reductase: transcriptional regulation of an atypical genomic organization in the nrd cluster. Microbiol SGM. 2003, 149: 1011-1020. 10.1099/mic.0.26133-0.
CAS
Google Scholar
Masalha M, Borovok I, Schreiber R, Aharonowitz Y, Cohen G: Analysis of transcription of the Staphylococcus aureus aerobic class Ib and anaerobic class III ribonucleotide reductase genes in response to oxygen. J Bacteriol. 2001, 183: 7260-7272. 10.1128/JB.183.24.7260-7272.2001.
CAS
PubMed Central
PubMed
Google Scholar
Warner DF, Savvi S, Mizrahi V, Dawes SS: A riboswitch regulates expression of the coenzyme B-12-independent methionine synthase in Mycobacterium tuberculosis: Implications for differential methionine synthase function in strains H37Rv and CDC1551. J Bacteriol. 2007, 189: 3655-3659. 10.1128/JB.00040-07.
CAS
PubMed Central
PubMed
Google Scholar
Bailey S, Clokie MRJ, Millard A, Mann NH: Cyanophage infection and photoinhibition in marine cyanobacteria. Res Microbiol. 2004, 155: 720-725. 10.1016/j.resmic.2004.06.002.
CAS
PubMed
Google Scholar
Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW: Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol. 2010, 12: 3035-3056. 10.1111/j.1462-2920.2010.02280.x.
CAS
PubMed Central
PubMed
Google Scholar
Bechhofer DH, Hue KK, Shub DA: An Intron in the thymidylate synthase gene of Bacillus bacteriophage-beta-22 - Evidence for independent evolution of a gene, its group-I intron, and the intron open reading frame. PNAS. 1994, 91: 11669-11673. 10.1073/pnas.91.24.11669.
CAS
PubMed Central
PubMed
Google Scholar
Chu FK, Maley GF, Maley F, Belfort M: Intervening sequence in the thymidylate synthase gene of bacteriophage-T4. PNAS Biol Sci. 1984, 81: 3049-3053.
CAS
Google Scholar
Goodrichblair H, Shub DA: The DNA polymerase genes of several Hmu-bacteriophages have similar group-I introns with highly divergent open reading frames. Nucleic Acids Res. 1994, 22: 3715-3721. 10.1093/nar/22.18.3715.
CAS
Google Scholar
Gott JM, Shub DA, Belfort M: Multiple self-splicing introns in bacteriophage-T4 - Evidence from autocatalytic GTP labeling of RNA in vitro. Cell. 1986, 47: 81-87. 10.1016/0092-8674(86)90368-5.
CAS
PubMed
Google Scholar
Landthaler M, Begley U, Lau NC, Shub DA: Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort. Nucleic Acids Res. 2002, 30: 1935-1943. 10.1093/nar/30.9.1935.
CAS
PubMed Central
PubMed
Google Scholar
Mikkonen M, Alatossava T: A group-I intron in the terminase gene of Lactobacillus-Delbrueckii subsp. lactis phage Ll-H. Microbiol UK. 1995, 141: 2183-2190. 10.1099/13500872-141-9-2183.
CAS
Google Scholar
Sjoberg BM, Hahne S, Mathews CZ, Mathews CK, Rand KN, Gait MJ: The bacteriophage-T4 gene for the small subunit of ribonucleotide reductase contains an intron. EMBO J. 1986, 5: 2031-2036.
CAS
PubMed Central
PubMed
Google Scholar
VanSinderen D, Karsens H, Kok J, Terpstra P, Ruiters MHJ, Venema G, Nauta A: Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol Microbiol. 1996, 19: 1343-1355. 10.1111/j.1365-2958.1996.tb02478.x.
CAS
Google Scholar
Young C, Bechhofer DH, Figurski DH: Gene-regulation in plasmid-Rk2 - Positive control by Kora in the expression of Korc. J Bacteriol. 1984, 157: 247-252.
CAS
PubMed Central
PubMed
Google Scholar
Derbyshire V, Belfort M: Lightning strikes twice: Intron-intein coincidence. PNAS. 1998, 95: 1356-1357. 10.1073/pnas.95.4.1356.
CAS
PubMed Central
PubMed
Google Scholar
Lazarevic V, Soldo B, Dusterhoft A, Hilbert H, Mauel C, Karamata D: Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SP beta. PNAS. 1998, 95: 1692-1697. 10.1073/pnas.95.4.1692.
CAS
PubMed Central
PubMed
Google Scholar
Belfort M: Scientific serendipity initiates an intron odyssey. J Biol Chem. 2009, 284: 29997-30003. 10.1074/jbc.X109.055400.
CAS
PubMed Central
PubMed
Google Scholar
Edgell DR, Belfort M, Shub DA: Barriers to intron promiscuity in bacteria. J Bacteriol. 2000, 182: 5281-5289. 10.1128/JB.182.19.5281-5289.2000.
CAS
PubMed Central
PubMed
Google Scholar
Belle A, Landthaler M, Shub DA: Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Gene Dev. 2002, 16: 351-362. 10.1101/gad.960302.
CAS
PubMed Central
PubMed
Google Scholar
Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM: Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage. J Bacteriol. 2003, 185: 5220-5233. 10.1128/JB.185.17.5220-5233.2003.
CAS
PubMed Central
PubMed
Google Scholar
Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S: Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res. 2009, 37: 2560-2573. 10.1093/nar/gkp095.
CAS
PubMed Central
PubMed
Google Scholar
Kutter E, Gachechiladze K, Poglazov A, Marusich E, Shneider M, Aronsson P, Napuli A, Porter D, Mesyanzhinov V: Evolution of T4-related phages. Virus Genes. 1995, 11: 285-297. 10.1007/BF01728666.
CAS
PubMed
Google Scholar
Sandegren L, Nord D, Sjoberg BM: SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages. Nucleic Acids Res. 2005, 33: 6203-6213. 10.1093/nar/gki932.
CAS
PubMed Central
PubMed
Google Scholar
Young P, Ohman M, Xu MQ, Shub DA, Sjoberg BM: Intron-containing T4-bacteriophage gene Suny encodes an anaerobic ribonucleotide reductase. J Biol Chem. 1994, 269: 20229-20232.
CAS
PubMed
Google Scholar
Friedrich NC, Torrents E, Gibb EA, Sahlin M, Sjoberg BM, Edgell DR: Insertion of a homing endonuclease creates a genes-in-pieces ribonudeotide reductase that retains function. PNAS. 2007, 104: 6176-6181. 10.1073/pnas.0609915104.
CAS
PubMed Central
PubMed
Google Scholar
Kim JH, Son JS, Choi YJ, Choresca CH, Shin SP, Han JE, Jun JW, Park SC: Complete genomic sequence of a T4-like bacteriophage, phiAS4, infecting Aeromonas salmonicida subsp. salmonicida. Arch Virol. 2012, 157: 391-395. 10.1007/s00705-011-1175-9.
CAS
PubMed
Google Scholar
Klumpp J, Dorscht J, Lurz R, Bielmann R, Wieland M, Zimmer M, Calendar R, Loessner MJ: The terminally redundant, nonpermuted genome of Listeria bacteriophage A511: a model for the SPO1-like myoviruses of gram-positive bacteria. J Bacteriol. 2008, 190: 5753-5765. 10.1128/JB.00461-08.
CAS
PubMed Central
PubMed
Google Scholar
Carlton RM, Noordman WH, Biswas B, de Meester ED, Loessner MJ: Bacteriophage P100 for control of Listeria monocytogenes in foods: Genome sequence, bioinformatic analyses, oral toxicity study, and application. RegulToxicol Pharm. 2005, 43: 301-312.
CAS
Google Scholar
Kilcher S, Loessner MJ, Klumpp J: Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. J Bacteriol. 2010, 192: 5441-5453. 10.1128/JB.00709-10.
CAS
PubMed Central
PubMed
Google Scholar
Collins MD, Wallbanks S, Lane DJ, Shah J, Nietupski R, Smida J, Dorsch M, Stackebrandt E: Phylogenetic analysis of the genus Listeria based on reverse-transcriptase sequencing of 16S ribosomal-RNA. Int J Syst Bacteriol. 1991, 41: 240-246. 10.1099/00207713-41-2-240.
CAS
PubMed
Google Scholar
Sandegren L, Sjoberg BM: Self-splicing of the bacteriophage T4 group I introns requires efficient translation of the pre-mRNA in vivo and correlates with the growth state of the infected bacterium. J Bacteriol. 2007, 189: 980-990. 10.1128/JB.01287-06.
CAS
PubMed Central
PubMed
Google Scholar
Timms AR, Cambray-Young J, Scott AE, Petty NK, Connerton PL, Clarke L, Seeger K, Quail M, Cummings N, Maskell DJ, Thomson NR, Connerton IF: Evidence for a lineage of virulent bacteriophages that target Campylobacter. BMC Genomics. 2010, 11: 214-224. 10.1186/1471-2164-11-214.
PubMed Central
PubMed
Google Scholar
Carvalho CM, Kropinski AM, Lingohr EJ, Santos SB, King J, Azeredo J: The genome and proteome of a Campylobacter coli bacteriophage vB_CcoM-IBB_35 reveal unusual features. Virol J. 2012, 9: 35-45. 10.1186/1743-422X-9-35.
CAS
PubMed Central
PubMed
Google Scholar
Sakaguchi Y, Hayashi T, Kurokawa K, Nakayama K, Oshima K, Fujinaga Y, Ohnishi M, Ohtsubo E, Hattori M, Oguma K: The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. PNAS. 2005, 102: 17472-17477. 10.1073/pnas.0505503102.
CAS
PubMed Central
PubMed
Google Scholar
Naryshkina T, Liu J, Florens L, Swanson SK, Pavlov AR, Pavlova NV, Inman R, Minakhin L, Kozyavkin SA, Washburn M, Mushegian A, Severinov K: Thermus thermophilus bacteriophage phi YS40 genome and proteomic characterization of virions. J Biol Evol. 2006, 364: 667-677.
CAS
Google Scholar
Chen CL, Pan TY, Kan SC, Kuan YC, Hong LY, Chiu KR, Sheu CS, Yang JS, Hsu WH, Hu HY: Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: Evolutionary relationships to phages from Corynebacterineae. Virology. 2008, 378: 226-232. 10.1016/j.virol.2008.05.027.
CAS
PubMed
Google Scholar
Samson JE, Moineau S: Characterization of Lactococcus lactis phage 949 and comparison with other lactococcal phages. Appl Environ Microbiol. 2010, 76: 6843-6852. 10.1128/AEM.00796-10.
CAS
PubMed Central
PubMed
Google Scholar
Crutz-Le Coq AM, Cesselin B, Commissaire J, Anba J: Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Microbiol SGM. 2002, 148: 985-1001.
CAS
Google Scholar
Pride DT, Wassenaar TM, Ghose C, Blaser MJ: Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genomics. 2006, 7: 13-10.1186/1471-2164-7-13.
Google Scholar
Williamson SJ, Cary SC, Williamson KE, Helton RR, Bench SR, Winget D, Wommack KE: Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J. 2008, 2: 1112-1121. 10.1038/ismej.2008.73.
CAS
PubMed
Google Scholar
Burge C, Campbell AM, Karlin S: Over-representation and under-representation of short oligonucleotides in DNA-sequences. PNAS. 1992, 89: 1358-1362. 10.1073/pnas.89.4.1358.
CAS
PubMed Central
PubMed
Google Scholar
Gilbert JA, Field D, Huang Y, Edwards R, Li WZ, Gilna P, Joint I: Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One. 2008, 3: e3042-e3055. 10.1371/journal.pone.0003042.
PubMed Central
PubMed
Google Scholar
Kim KH, Bae JW: Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol. 2011, 77: 7663-7668. 10.1128/AEM.00289-11.
CAS
PubMed Central
PubMed
Google Scholar
Shendure J, Ji HL: Next-generation DNA sequencing. Nat Biotechnol. 2008, 26: 1135-1145. 10.1038/nbt1486.
CAS
PubMed
Google Scholar
Wooley JC, Godzik A, Friedberg I: A Primer on metagenomics. PLoS Comput Biol. 2010, 6: e1000667-10.1371/journal.pcbi.1000667.
PubMed Central
PubMed
Google Scholar
Rosario K, Breitbart M: Exploring the viral world through metagenomics. Curr Opin Virol. 2011, 1: 289-297. 10.1016/j.coviro.2011.06.004.
CAS
PubMed
Google Scholar
Kim KH, Chang HW, Nam YD, Roh SW, Kim MS, Sung Y, Jeon CO, Oh HM, Bae JW: Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol. 2008, 74: 5975-5985. 10.1128/AEM.01275-08.
CAS
PubMed Central
PubMed
Google Scholar
Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P, Rohwer F: Diversity and population structure of a near-shore marine-sediment viral community. P Roy Soc B-Biol Sci. 2004, 271: 565-574. 10.1098/rspb.2003.2628.
Google Scholar
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F: Genomic analysis of uncultured marine viral communities. PNAS. 2002, 99: 14250-14255. 10.1073/pnas.202488399.
CAS
PubMed Central
PubMed
Google Scholar
Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan YJ, Hall D, Angly FE, Edwards RA, Li LL, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F: Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature. 2008, 452: 340-343. 10.1038/nature06735.
CAS
PubMed
Google Scholar
Rodriguez-Brito B, Li LL, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, Felts B, Haynes M, Liu H, Lipson D, Mahaffy J, Martin-Cuadrado AB, Mira A, Nulton J, Pasic L, Rayhawk S, Rodriguez-Mueller J, Rodriguez-Valera F, Salamon P, Srinagesh S, Thingstad TF, Tran T, Thurber RV, Willner D, Youle M, Rohwer F: Viral and microbial community dynamics in four aquatic environments. ISME J. 2010, 4: 739-751. 10.1038/ismej.2010.1.
PubMed
Google Scholar
Santos F, Meyerdierks A, Pena A, Rossello-Mora R, Amann R, Anton J: Metagenomic approach to the study of halophages: the environmental halophage 1. Environ Microbiol. 2007, 9: 1711-1723. 10.1111/j.1462-2920.2007.01289.x.
CAS
PubMed
Google Scholar
Santos F, Yarza P, Parro V, Briones C, Anton J: The metavirome of a hypersaline environment. Environ Microbiol. 2010, 12: 2965-2976. 10.1111/j.1462-2920.2010.02273.x.
CAS
PubMed
Google Scholar
Parsley LC, Consuegra EJ, Thomas SJ, Bhavsar J, Land AM, Bhuiyan NN, Mazher MA, Waters RJ, Wommack KE, Harper WF, Liles MR: Census of the viral metagenome within an activated sludge microbial assemblage. Appl Environ Microbiol. 2010, 76: 2673-2677. 10.1128/AEM.02520-09.
CAS
PubMed Central
PubMed
Google Scholar
Sime-Ngando T, Lucas S, Robin A, Tucker KP, Colombet J, Bettarel Y, Desmond E, Gribaldo S, Forterre P, Breitbart M, Prangishvili D: Diversity of virus-host systems in hypersaline lake Retba. Senegal. Environ Microbiol. 2011, 13: 1956-1972. 10.1111/j.1462-2920.2010.02323.x.
Google Scholar
Anderson RE, Brazelton WJ, Baross JA: Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol Ecol. 2011, 77: 120-133. 10.1111/j.1574-6941.2011.01090.x.
CAS
PubMed
Google Scholar
Thurber RLV, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL: Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. PNAS. 2008, 105: 18413-18418. 10.1073/pnas.0808985105.
Google Scholar
Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A: High diversity of the viral community from an Antarctic lake. Science. 2009, 326: 858-861. 10.1126/science.1179287.
CAS
PubMed
Google Scholar
Rho MN, Tang HX, Ye YZ: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010, 38: e191-e203. 10.1093/nar/gkq747.
PubMed Central
PubMed
Google Scholar
Finn RD, Clements J, Eddy SR: HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011, 39: W29-W37. 10.1093/nar/gkr367.
CAS
PubMed Central
PubMed
Google Scholar
Marchler-Bauer A, Lu SN, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke ZX, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang DC, Zhang NG, Zheng CJ, Bryant SH: CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39: D225-D229. 10.1093/nar/gkq1189.
CAS
PubMed Central
PubMed
Google Scholar
Perler FB: InBase: The intein database. Nucleic Acids Res. 2002, 30: 383-384. 10.1093/nar/30.1.383.
CAS
PubMed Central
PubMed
Google Scholar
Simossis VA, Heringa J: PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 2005, 33: W289-W294. 10.1093/nar/gki390.
CAS
PubMed Central
PubMed
Google Scholar
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552. 10.1093/oxfordjournals.molbev.a026334.
CAS
PubMed
Google Scholar
Talavera G, Castresana J: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007, 56: 564-577. 10.1080/10635150701472164.
CAS
PubMed
Google Scholar
Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080/10635150390235520.
PubMed
Google Scholar
Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005, 21: 2104-2105. 10.1093/bioinformatics/bti263.
CAS
PubMed
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28: 2731-2739. 10.1093/molbev/msr121.
CAS
PubMed Central
PubMed
Google Scholar
Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, Wang K, Wommack KE: Metagenomic characterization of Chesapeake bay virioplankton. Appl Environ Microbiol. 2007, 73: 7629-7641. 10.1128/AEM.00938-07.
CAS
PubMed Central
PubMed
Google Scholar
McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F, Paul JH: Metagenomic analysis of lysogeny in Tampa bay: Implications for prophage gene expression. PLoS One. 2008, 3: e3263-e3272. 10.1371/journal.pone.0003263.
PubMed Central
PubMed
Google Scholar
Marhaver KL, Edwards RA, Rohwer F: Viral communities associated with healthy and bleaching corals. Environ Microbiol. 2008, 10: 2277-2286. 10.1111/j.1462-2920.2008.01652.x.
CAS
PubMed Central
PubMed
Google Scholar
Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D: Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol. 2010, 18: 20-29. 10.1016/j.tim.2009.10.001.
CAS
PubMed Central
PubMed
Google Scholar
Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M: Metagenomic analysis of viruses in reclaimed water. Environmental Microbiology. 2009, 11: 2806-2820. 10.1111/j.1462-2920.2009.01964.x.
CAS
PubMed
Google Scholar
Kunin V, He S, Warnecke F, Peterson SB, Martin HG, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD, Hugenholtz P: A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res. 2008, 18: 293-297. 10.1101/gr.6835308.
CAS
PubMed Central
PubMed
Google Scholar
Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB: Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol. 2007, 73: 7059-7066. 10.1128/AEM.00358-07.
CAS
PubMed Central
PubMed
Google Scholar
Park EJ, Kim KH, Abell GCJ, Kim MS, Roh SW, Bae JW: Metagenomic analysis of the viral communities in fermented foods. Appl Environ Microbiol. 2011, 77: 1284-1291. 10.1128/AEM.01859-10.
CAS
PubMed Central
PubMed
Google Scholar