Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Virology. 2015 Mar;477:144-154. doi: 10.1016/j.virol.2014.10.016. Epub 2014 Nov 14.

Abstract

Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.

Keywords: ClustalW; CoreGenes; ICTV; Phage Proteomic Tree; Siphoviridae; Taxonomy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophages / chemistry
  • Bacteriophages / classification*
  • Bacteriophages / genetics
  • Genome, Viral*
  • Genomics / methods
  • Proteome / analysis*
  • Proteomics / methods
  • Siphoviridae / chemistry
  • Siphoviridae / classification*
  • Siphoviridae / genetics
  • Viral Proteins / analysis*
  • Virology / methods

Substances

  • Proteome
  • Viral Proteins