Unifying classical and molecular taxonomic classification:: analysis of the Podoviridae using BLASTP-based tools

被引：247

作者：

Lavigne, Rob ^{[3
]}

Seto, Donald ^{[4
]}

Mahadevan, Padmanabhan ^{[4
]}

Ackermann, Hans-W. ^{[5
]}

Kropinski, Andrew M. ^{[1
,2
]}

机构：

[1] Publ Hlth Agcy Canada, Lab Foodborne Zoonoses, Guelph, ON N1G 3W4, Canada

[2] Univ Guelph, Dept Mol & Cellular Biol, Guelph, ON N1G 2W1, Canada

[3] Katholieke Univ Leuven, Lab Gene Technol, B-3001 Louvain, Belgium

[4] George Mason Univ, Dept Bioinformat & Computat Biol, Manassas, VA 20110 USA

[5] Univ Laval, Fac Med, Dept Med Biol, Felix DHerelle Ref Ctr Bacterial Viruses, Quebec City, PQ G1K 4C6, Canada

来源：

RESEARCH IN MICROBIOLOGY | 2008年 / 159卷 / 05期

基金：

加拿大自然科学与工程研究理事会;

关键词：

Autographivirinae; bacteriophage; BLAST; CoreGenes; CoreExtractor; Nanovirinae; P22; Podoviridae T7; Taxonomy; virus; phi; 29;

D O I：

10.1016/j.resmic.2008.03.005

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the (phi 29-related phages, and introduced five novel genera. The T7- and (phi 29-related phages were given subfamily status and named "Autographivirinae" and "Picovirinae", respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes. Crown Copyright (C) 2008 Published by Elsevier Masson SAS. All rights reserved.

引用

页码：406 / 414

页数：9

共 62 条

[41] Genomic structure of the Salmonella enterica serovar Typhimurium DT 64 bacteriophage ST64T:: Evidence for modular genetic architecture [J].

Mmolawa, PT ;

Schmieger, H ;

Tucker, CP ;

Heuzenroeder, MW .

JOURNAL OF BACTERIOLOGY, 2003, 185 (11) :3473-3475

[42] Bacteriophage φYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7 [J].

Pajunen, M ;

Kiljunen, S ;

Skurnik, M .

JOURNAL OF BACTERIOLOGY, 2000, 182 (18) :5114-5120

[43] Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3 [J].

Pajunen, MI ;

Elizondo, MR ;

Skurnik, M ;

Kieleczawa, J ;

Molineux, IJ .

JOURNAL OF MOLECULAR BIOLOGY, 2002, 319 (05) :1115-1132

[44]

Pecenkova T, 1997, GENE, V199, P157

[45] Corrected sequence of the bacteriophage P22 genome [J].

Pedulla, ML ;

Ford, ME ;

Karthikeyan, T ;

Houtz, JM ;

Hendrix, RW ;

Hatfull, GF ;

Poteete, AR ;

Gilcrease, EB ;

Winn-Stapley, DA ;

Casjens, SR .

JOURNAL OF BACTERIOLOGY, 2003, 185 (04) :1475-1477

[46] The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages [J].

Rohwer, F ;

Segall, A ;

Steward, G ;

Seguritan, V ;

Breitbart, M ;

Wolven, F ;

Azam, F .

LIMNOLOGY AND OCEANOGRAPHY, 2000, 45 (02) :408-418

[47] The Phage Proteomic Tree: a genome-based taxonomy for phage [J].

Rohwer, F ;

Edwards, R .

JOURNAL OF BACTERIOLOGY, 2002, 184 (16) :4529-4535

[48]

Salas M., 2006, The Bacteriophages, chapter 22, V29 and its relatives, P315

[49] The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli [J].

Scholl, D ;

Merril, C .

JOURNAL OF BACTERIOLOGY, 2005, 187 (24) :8499-8503

[50] Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli [J].

Scholl, D ;

Rogers, S ;

Adhya, S ;

Merril, CR .

JOURNAL OF VIROLOGY, 2001, 75 (06) :2509-2515

← 1 2 3 4 5 6 7 →