Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools.
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 phi29-related phages, and introduced five novel genera. The T7- and phi29-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.
Lavigne
Rob
R
Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium.
Seto
Donald
D
Mahadevan
Padmanabhan
P
Ackermann
Hans-W
HW
Kropinski
Andrew M
AM
D030541:Databases, Genetic; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D017902:Podoviridae / Q000145:classification* / Q000235:genetics*; D040901:Proteomics; D017422:Sequence Analysis, DNA