Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.
The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Welkin H
WH
Pope
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Charles A
CA
Bowman
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Daniel A
DA
Russell
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Deborah
D
Jacobs-Sera
Howard Hughes Medical Institute, Chevy Chase, United States.
David J
DJ
Asai
Department of Biology, James Madison University, Harrisonburg, United States.
Steven G
SG
Cresawn
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States.
William R
WR
Jacobs
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Roger W
RW
Hendrix
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Jeffrey G
JG
Lawrence
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States.
Graham F
GF
Hatfull
D035843:Biomedical Research / Q000941:ethics; D003299:Cooperative Behavior; D004279:DNA, Viral / Q000235:genetics*; D051456:Gene Flow; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D033181:Information Dissemination; D009030:Mosaicism; D009160:Mycobacteriophages / Q000145:classification / Q000235:genetics*; D020102:Mycobacterium smegmatis / Q000821:virology; D010802:Phylogeny; D058974:Phylogeography; D000078329:Workforce
D004279:DNA, Viral
bacteriophage; evolution; evolutionary biology; genomics; infectious disease; microbiology; viruses