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

[1] 5500 Phages examined in the electron microscope [J].

Ackermann, H. -W. .

ARCHIVES OF VIROLOGY, 2007, 152 (02) :227-243

[2]

Ackermann HW, 2005, BACTERIOPHAGE: BIOLOGY AND APPLICATIONS, P67

[3] MORPHOLOGY OF PSEUDOMONAS-AERUGINOSA TYPING PHAGES OF THE LINDBERG SET [J].

ACKERMANN, HW ;

CARTIER, C ;

SLOPEK, S ;

VIEU, JF .

ANNALES DE L INSTITUT PASTEUR-VIROLOGY, 1988, 139 (04) :389-404

[4]

Adams MJ, 2004, ARCH VIROL, V149, P1045, DOI [10.1007/s00705-003-0304-0, 10.1007/s00705-004-0304-0]

[5] Molecular criteria for genus and species discrimination within the family Potyviridae [J].

Adams, MJ ;

Antoniw, JF ;

Fauquet, CM .

ARCHIVES OF VIROLOGY, 2005, 150 (03) :459-479

[6]

Bernstein C., 1983, BACTERIOPHAGE T4, P138

[7] Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa [J].

Braid, MD ;

Silhavy, JL ;

Kitts, CL ;

Cano, RJ ;

Howe, MM .

JOURNAL OF BACTERIOLOGY, 2004, 186 (19) :6560-6574

[8] Phage genomics:: Small is beautiful [J].

Brüssow, H ;

Hendrix, RW .

CELL, 2002, 108 (01) :13-16

[9] The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116 [J].

Byrne, M ;

Kropinski, AM .

GENE, 2005, 346 :187-194

[10] The chromosome of Shigella flexneri bacteriophage Sf6:: Complete nucleotide sequence, genetic mosaicism, and DNA packaging [J].

Casjens, S ;

Winn-Stapley, DA ;

Gilcrease, EB ;

Morona, R ;

Kühlewein, C ;

Chua, JEH ;

Manning, PA ;

Inwood, W ;

Clark, AJ .

JOURNAL OF MOLECULAR BIOLOGY, 2004, 339 (02) :379-394

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