Mycobacteriophage CRB2 defines a new subcluster in mycobacteriophage classification

PLoS One. 2019 Feb 27;14(2):e0212365. doi: 10.1371/journal.pone.0212365. eCollection 2019.

Abstract

Mycobacteriophages are viruses -mostly temperates- that infect Mycobacterium smegmatis and sometimes Mycobacterium tuberculosis. Mycobacteriophages are grouped in clusters on the basis of the overall nucleotide sequence homology, being further divided in subclusters as more mycobacteriophage genomes are sequenced and annotated. As part of our on-going screening for novel isolates, we herein report the bioinformatics analysis of CRB2, a mycobacteriophage belonging into the Siphoviridae family that propagates at 30°C. CRB2 has a 72,217 bp genome with a 69.78% GC content that belongs to Cluster B; nucleotide comparison with other B cluster members positions CRB2 as the sole member of a new subcluster, B9, being mycobacteriophage Saguaro (belonging into subcluster B7) its closest relative. Sequencing and annotation of 14 mycobacteriophages isolated by our group has yielded six cluster A members, a singleton, four of the five members of subcluster B6, one of the three reported members of subcluster G4, and CRB2 which defines subcluster B9. Considering the massive mycobacteriophage search performed in USA and the relatively rarity of our phages, we propose that factors other than size of the sampling determine the variability of mycobacteriophage distribution, and thus a world-wide concerted mining would most likely bring extremely rare and yet undiscovered mycobacteriophages.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodiversity*
  • Codon / genetics*
  • DNA, Viral / genetics*
  • Genome, Viral*
  • Mycobacteriophages / classification*
  • Mycobacteriophages / genetics*
  • Mycobacteriophages / isolation & purification
  • Mycobacterium tuberculosis / virology*
  • Phylogeny

Substances

  • Codon
  • DNA, Viral

Grants and funding

This work was supported by grants (PICT 02337 and PICT 1406 to HRM) from the National Agency for Science and Technology Promotion (ANPCyT), Argentina. HRM is a career member of Consejo de Investigaciones de la Universidad Nacional de Rosario (CIUNR), CAS and JJF are careerr member and post-doctoral fellow of Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.