TY - JOUR
T1 - Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity
AU - Pope, Welkin H.
AU - Bowman, Charles A.
AU - Russell, Daniel A.
AU - Jacobs-Sera, Deborah
AU - Asai, David J.
AU - Cresawn, Steven G.
AU - Jacobs, William R.
AU - Hendrix, Roger W.
AU - Lawrence, Jeffrey G.
AU - Hatfull, Graham F.
N1 - Funding Information:
Students, faculty, and their contributions to authorship are listed in the Supplementary file 2. We thank Aileen Beard, Gerald Henkel-Johnson, and Larry McGahey at the College of St. Scholastica, the Core Facility for Imaging, Cellular and Molecular Biology at Queens College, Jennifer Kelly and Towanda Kirksey-Stanton at Jacksonville State Univeristy, Susan Crump at Merrimack College and Dr Gregory Hendricks at the University of Massachusetts Medical School Electron Microscopy Imaging Facility, Melissa Cox at North Carolina State University and Valerie Lapham at the NCSU Center for Electron Microscopy, Dr Karen M Snetselaar at Saint Joseph’s University, and Rick Ellingworth at the University of Wisconsin-River Falls for excellent technical assistance. We also thank Drs Winston Anderson and Broderick Eribo for their roles as consultants at Howard University, and Dr R Edelmann and the Miami University Center for Advanced Microscopy and Imaging for their support and assistance with electron microscopy. We also thank John Morrell, Alicia Brighton, Joshua Fisher, Michael Shelfo, Brigham Wright, Jessica Engle, Brian Early, Kyle Smith, Kyler Haskell, Tambi Issac, Bryce Lunt, David Payne II, Lissenya Argueta, Bryan Merrill, Adam Gardner, Hailey Meadows, Adam Hansen, and Marshall Sheide for contributions to phage isolation. This work was supported in part by the Howard Hughes Medical Institute SEA-PHAGES program, by the Howard Hughes Medical Institute through its Professorship grant to GFH, and by NIH grant GM51975 to GFH. Additional support was provided by the Department of Microbiology and Molecular Biology and the BYU College of Life Sciences; Cabrini College; NIH Grant No. P20 GM103408 to the College of Idaho; the National Science Foundation grant 0703449, the CUNY LSAMP program, the Office of the Provost, the Division of General Education, the Division of Mathematics and Natural Sciences, the Queens College UM/RE program and the Biology Department at Queens College; the Department of Biological Sciences at Lehigh University; the Center for Biotechnology and Biomedical Sciences of the Department of Biology in the School of Science and Engineering at Merrimack College; the NCSU Biotechnology Program and Department of Microbiology; a Davis Foundation grant, the Providence College Undergraduate Research Committee, RI-INBRE and NIGMS grant R15-GM094712 to Providence College; the Department of Biology, Saint Joseph’s University; the Natural Science Department at the University of Houston-Downtown; the University of Maine Honors College, the University of Maine Department of Molecular and Biomedical Sciences, Maine-INBRE and NIH-INBRE Grant 8P20GM1003423-12; an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health (P20GM0103423) to the University of Maine at Machias; the Howard Hughes Medical Institute, RISE and BRIC Programs, the Department of Biology, and the Offices of the Academic Dean and Chancellor at the University of Puerto Rico at Cayey; the University of Wisconsin River Falls Biology Department; the Gatton Academy of Science and Mathematics in Kentucky and the Western Kentucky University Bioinformatics and Information Science Center; Georgia College STEM Initiative and a Georgia College Faculty Research Grant; NSF Grant REVISION DUE-1205059 and the Department of Natural Sciences at Del Mar College; Miami University Department of Microbiology and the College of Arts and Science Dean’s office and National Science Foundation ABI award 1146960; the HHMI Scicomp Project (52007572) to Xavier University of Louisiana; the Doris Duke Foundation; the Gonzaga University Biology Department, NSF-TUES grant DUE-1245778 and HHMI Undergraduate Science Education grant to Gonzaga University; the School of Biological Sciences and the School of Molecular Biosciences at Washington State University; and the Benjamin Harris Memorial Fund through the Pittsburgh Foundation.
Funding Information:
Howard Hughes Medical Institute (HHMI) -54308198- Graham F Hatfull, National Institutes of Health (NIH) - GM51975 - Graham F Hatfull, Howard Hughes Medical Institute (HHMI) ? 52007054 - Graham F Hatfull, Brigham Young University - Sandra Burnett, Cabrini College- David Dunbar, National Institutes of Health?INBRE - GM103408- R Luke Daniels, 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) - GM100342 - 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 Hatherillm 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 Anders.
Publisher Copyright:
© Pope et al.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
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U2 - 10.7554/eLife.06416
DO - 10.7554/eLife.06416
M3 - Article
C2 - 25919952
AN - SCOPUS:85018215086
SN - 2050-084X
VL - 4
JO - eLife
JF - eLife
M1 - e06416
ER -