Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

By W. Pope, Charles A. Bowman, Daniel A. Russell, D. Jacobs-Sera, David J. Asai, Steven G. Cresawn, W. R. Jacobs, R. Hendrix, Jeffrey G. Lawrence, Graham F. Hatfull and 1 more. 2015

285 citations recorded by the source corpus.

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. DOI: http://dx.doi.org/10.7554/eLife.06416.001

Subfields: Ecology, Epidemiology, Microbiology

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In Ecology

1. Graham F. Hatfull
2. V. M. Villanueva
3. Lauren M. Oldfield
4. Travis N. Mavrich

In Epidemiology

1. V. M. Villanueva
2. Lauren M. Oldfield
3. Graham F. Hatfull

Citations in the corpus

• An Unusual Phage Repressor Encoded by Mycobacteriophage BPs (2015, background): “Comparative genomic analysis of a large number of completely sequenced mycobacteriophages shows them to be highly diverse, and they can be grouped into ‘clusters’ according to their nucleotide and gene content relationships [14, 15].”