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

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dc.contributorKolter, Roberto
dc.contributor.authorPope, Welkin H.
dc.contributor.authorBowman, Charles A.
dc.contributor.authorRussell, Daniel A.
dc.contributor.authorJacobs-Sera, Deborah
dc.contributor.authorAsai, David J.
dc.contributor.authorCresawn, Steven G.
dc.contributor.authorJacobs Jr, William R.
dc.contributor.authorHendrix, Roger W.
dc.contributor.authorLawrence, Jeffrey G.
dc.contributor.authorHatfull, Graham F.
dc.contributor.authorCaruso, Steven
dc.contributor.authorScience Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science
dc.contributor.authorPhage Hunters Integrating Research and Education, Mycobacterial Genetics Course
dc.date.accessioned2019-04-02T15:00:46Z
dc.date.available2019-04-02T15:00:46Z
dc.date.issued2015-04-28
dc.descriptionSteven Caruso is a member of Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Scienceen_US
dc.description.abstractThe 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.en_US
dc.description.sponsorshipBelow are the sponsors : National Science Foundation (NSF) - John Dennehy Queens College - John Dennehy Lehigh University - Vassie Ware Merrimack College - Janine LeBlanc-Straceski National Institutes of Health (NIH) GM094712 - Nicanor Austriaco National Institutes of Health—INBRE GM103430 - Kathleen Cornely Davis Foundational Grant - Kathleen Cornely Providence College - Kathleen Cornely St. Joseph’s University - Christina King Smith University of Houston, Downtown -Rachna Sadana University of Maine, Honors College - Keith Hutchinson National Institutes of Health (NIH) GM1003423 - Keith Hutchinson Howard Hughes Medical Institute (HHMI) Michael Rubin, Kirk Anders, SEA-PHAGES program University of Puerto Rico - Michael Rubin University of Wisconsin, River Falls -Karen Klyczek Western Kentucky University - Claire Rinehart Gatton Academy of Science and Mathematics - Rodney King Georgia College - Indiren Pillay Del Mar College - John Hatherill Miami University - Iddo Friedberg National Science Foundation (NSF) DUE-1205059 John Hatherill National Science Foundation (NSF) ABI-1146960 Iddo Friedberg Howard Hughes Medical Institute (HHMI) 52007572 SK Ireland Doris Duke Charitable Foundation Michelle Larsen Gonzaga University Kirk Anders National Science Foundation (NSF) DUE-1245778 Kirk Andersen_US
dc.description.urihttps://elifesciences.org/articles/06416en_US
dc.format.extent65 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2wuxp-f2jk
dc.identifier.citationWelkin H Pope, Charles A Bowman, et.al, Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity, Pope et al. eLife 2015;4:e06416. DOI: 10.7554/eLife.06416en_US
dc.identifier.urihttps://doi.org/10.7554/eLife.06416
dc.identifier.urihttp://hdl.handle.net/11603/13298
dc.language.isoen_USen_US
dc.publishereLife Sciences Publications Ltden_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.subjectMycobacterium smegmatis
dc.subjectpervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness
dc.subjectrarefaction analysis
dc.subjectPhage isolation and analysis
dc.titleWhole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversityen_US
dc.typeTexten_US

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