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For: Monier A, Claverie JM, Ogata H. Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics 2007;8:456. [PMID: 18070355 PMCID: PMC2211322 DOI: 10.1186/1471-2164-8-456] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 12/10/2007] [Indexed: 12/02/2022]  Open
Number Cited by Other Article(s)
1
Witt ASA, Carvalho JVRP, Serafim MSM, Arias NEC, Rodrigues RAL, Abrahão JS. The GC% landscape of the Nucleocytoviricota. Braz J Microbiol 2024:10.1007/s42770-024-01496-7. [PMID: 39180708 DOI: 10.1007/s42770-024-01496-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024]  Open
2
Rahman MJ, Haller SL, Stoian AMM, Li J, Brennan G, Rothenburg S. LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses. eLife 2022;11:63327. [PMID: 36069678 PMCID: PMC9578709 DOI: 10.7554/elife.63327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/06/2022] [Indexed: 11/27/2022]  Open
3
Yau S, Krasovec M, Benites LF, Rombauts S, Groussin M, Vancaester E, Aury JM, Derelle E, Desdevises Y, Escande ML, Grimsley N, Guy J, Moreau H, Sanchez-Brosseau S, van de Peer Y, Vandepoele K, Gourbiere S, Piganeau G. Virus-host coexistence in phytoplankton through the genomic lens. SCIENCE ADVANCES 2020;6:eaay2587. [PMID: 32270031 PMCID: PMC7112755 DOI: 10.1126/sciadv.aay2587] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/09/2020] [Indexed: 05/02/2023]
4
Diversity and evolution of the emerging Pandoraviridae family. Nat Commun 2018;9:2285. [PMID: 29891839 PMCID: PMC5995976 DOI: 10.1038/s41467-018-04698-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/17/2018] [Indexed: 02/02/2023]  Open
5
Smithson C, Imbery J, Upton C. Re-Assembly and Analysis of an Ancient Variola Virus Genome. Viruses 2017;9:v9090253. [PMID: 28885569 PMCID: PMC5618019 DOI: 10.3390/v9090253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/17/2022]  Open
6
Ardisson-Araújo DMP, Lima RN, Melo FL, Clem RJ, Huang N, Báo SN, Sosa-Gómez DR, Ribeiro BM. Genome sequence of Perigonia lusca single nucleopolyhedrovirus: insights into the evolution of a nucleotide metabolism enzyme in the family Baculoviridae. Sci Rep 2016;6:24612. [PMID: 27273152 PMCID: PMC4895240 DOI: 10.1038/srep24612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/01/2016] [Indexed: 12/19/2022]  Open
7
Ardisson-Araújo DMP, Pereira BT, Melo FL, Ribeiro BM, Báo SN, de A Zanotto PM, Moscardi F, Kitajima EW, Sosa-Gomez DR, Wolff JLC. A betabaculovirus encoding a gp64 homolog. BMC Genomics 2016;17:94. [PMID: 26847652 PMCID: PMC4741009 DOI: 10.1186/s12864-016-2408-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/20/2016] [Indexed: 11/23/2022]  Open
8
Homology-independent metrics for comparative genomics. Comput Struct Biotechnol J 2015;13:352-7. [PMID: 26029354 PMCID: PMC4446528 DOI: 10.1016/j.csbj.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/06/2015] [Accepted: 04/18/2015] [Indexed: 11/24/2022]  Open
9
Pagarete A, Kusonmano K, Petersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA. Dip in the gene pool: metagenomic survey of natural coccolithovirus communities. Virology 2014;466-467:129-37. [PMID: 24947907 DOI: 10.1016/j.virol.2014.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
10
Gao C, Ren X, Mason AS, Liu H, Xiao M, Li J, Fu D. Horizontal gene transfer in plants. Funct Integr Genomics 2013;14:23-9. [PMID: 24132513 DOI: 10.1007/s10142-013-0345-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 01/12/2023]
11
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics 2013;14:537. [PMID: 23924250 PMCID: PMC3751351 DOI: 10.1186/1471-2164-14-537] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/03/2013] [Indexed: 11/10/2022]  Open
12
Claverie JM, Abergel C. Open questions about giant viruses. Adv Virus Res 2013;85:25-56. [PMID: 23439023 DOI: 10.1016/b978-0-12-408116-1.00002-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
13
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, de Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME JOURNAL 2013;7:1678-95. [PMID: 23575371 PMCID: PMC3749498 DOI: 10.1038/ismej.2013.59] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/28/2013] [Accepted: 03/06/2013] [Indexed: 11/17/2022]
14
Jeanniard A, Dunigan DD, Gurnon JR, Agarkova IV, Kang M, Vitek J, Duncan G, McClung OW, Larsen M, Claverie JM, Van Etten JL, Blanc G. Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses. BMC Genomics 2013;14:158. [PMID: 23497343 PMCID: PMC3602175 DOI: 10.1186/1471-2164-14-158] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/22/2013] [Indexed: 11/29/2022]  Open
15
Legendre M, Arslan D, Abergel C, Claverie JM. Genomics of Megavirus and the elusive fourth domain of Life. Commun Integr Biol 2012;5:102-6. [PMID: 22482024 DOI: 10.4161/cib.18624] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
16
Bertelli C, Greub G. Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms. Front Cell Infect Microbiol 2012;2:110. [PMID: 22919697 PMCID: PMC3423634 DOI: 10.3389/fcimb.2012.00110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 08/01/2012] [Indexed: 12/05/2022]  Open
17
Ienne S, Pappas G, Benabdellah K, González A, Zingales B. Horizontal gene transfer confers fermentative metabolism in the respiratory-deficient plant trypanosomatid Phytomonas serpens. INFECTION GENETICS AND EVOLUTION 2012;12:539-48. [PMID: 22293462 DOI: 10.1016/j.meegid.2012.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/11/2012] [Accepted: 01/14/2012] [Indexed: 11/28/2022]
18
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden AZ. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environ Microbiol 2012;14:162-76. [PMID: 21914098 PMCID: PMC3429862 DOI: 10.1111/j.1462-2920.2011.02576.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
19
Yu JF, Xiao K, Jiang DK, Guo J, Wang JH, Sun X. An integrative method for identifying the over-annotated protein-coding genes in microbial genomes. DNA Res 2011;18:435-49. [PMID: 21903723 PMCID: PMC3223076 DOI: 10.1093/dnares/dsr030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
20
Kuno S, Yoshida T, Kamikawa R, Hosoda N, Sako Y. The distribution of a phage-related insertion sequence element in the cyanobacterium, Microcystis aeruginosa. Microbes Environ 2011;25:295-301. [PMID: 21576885 DOI: 10.1264/jsme2.me10125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
21
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME JOURNAL 2011;5:1143-51. [PMID: 21248859 DOI: 10.1038/ismej.2010.210] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Claverie JM, Abergel C. Mimivirus: the emerging paradox of quasi-autonomous viruses. Trends Genet 2010;26:431-7. [PMID: 20696492 DOI: 10.1016/j.tig.2010.07.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/04/2010] [Accepted: 07/15/2010] [Indexed: 11/16/2022]
23
Zhang Q, Ma Q, Su D, Li Q, Yao W, Wang C. Identification of horizontal gene transfer and recombination of PsaA gene in streptococcus mitis group. Microbiol Immunol 2010;54:313-9. [PMID: 20536729 DOI: 10.1111/j.1348-0421.2010.00216.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
24
Villarreal LP. The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 2009;1178:194-232. [PMID: 19845639 DOI: 10.1111/j.1749-6632.2009.05020.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
25
Claverie JM, Abergel C. Mimivirus and its virophage. Annu Rev Genet 2009;43:49-66. [PMID: 19653859 DOI: 10.1146/annurev-genet-102108-134255] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
26
Villarreal LP, Witzany G. Viruses are essential agents within the roots and stem of the tree of life. J Theor Biol 2009;262:698-710. [PMID: 19833132 DOI: 10.1016/j.jtbi.2009.10.014] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 09/28/2009] [Accepted: 10/08/2009] [Indexed: 02/06/2023]
27
Ten good reasons not to exclude giruses from the evolutionary picture. Nat Rev Microbiol 2009;7:615; author reply 615. [PMID: 19561626 DOI: 10.1038/nrmicro2108-c3] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Fletcher GJ, Christopher S, Gnanamony M. Why does size matter for viruses – A new paradigm on viral size. Med Hypotheses 2009;73:133-7. [DOI: 10.1016/j.mehy.2009.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 02/17/2009] [Accepted: 02/21/2009] [Indexed: 10/20/2022]
29
Viruses manipulate the marine environment. Nature 2009;459:207-12. [PMID: 19444207 DOI: 10.1038/nature08060] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
30
Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc Natl Acad Sci U S A 2009;106:12826-31. [PMID: 19553209 DOI: 10.1073/pnas.0905115106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
31
Cortez D, Forterre P, Gribaldo S. A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol 2009;10:R65. [PMID: 19531232 PMCID: PMC2718499 DOI: 10.1186/gb-2009-10-6-r65] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 06/04/2009] [Accepted: 06/16/2009] [Indexed: 11/10/2022]  Open
32
The evolution of guanylyl cyclases as multidomain proteins: conserved features of kinase-cyclase domain fusions. J Mol Evol 2009;68:587-602. [PMID: 19495554 DOI: 10.1007/s00239-009-9242-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 04/21/2009] [Indexed: 12/30/2022]
33
Odom MR, Hendrickson RC, Lefkowitz EJ. Poxvirus protein evolution: family wide assessment of possible horizontal gene transfer events. Virus Res 2009;144:233-49. [PMID: 19464330 PMCID: PMC2779260 DOI: 10.1016/j.virusres.2009.05.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/12/2009] [Accepted: 05/12/2009] [Indexed: 02/03/2023]
34
Langille MGI, Brinkman FSL. Bioinformatic detection of horizontally transferred DNA in bacterial genomes. F1000 BIOLOGY REPORTS 2009;1:25. [PMID: 20948661 PMCID: PMC2920674 DOI: 10.3410/b1-25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
35
de Andrade Zanotto PM, Krakauer DC. Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites. PLoS One 2008;3:e3500. [PMID: 18941535 PMCID: PMC2567038 DOI: 10.1371/journal.pone.0003500] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 09/17/2008] [Indexed: 11/19/2022]  Open
36
Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H. Marine mimivirus relatives are probably large algal viruses. Virol J 2008;5:12. [PMID: 18215256 PMCID: PMC2245910 DOI: 10.1186/1743-422x-5-12] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 01/23/2008] [Indexed: 11/23/2022]  Open
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