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, w...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-04-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/06416 |
| _version_ | 1818019615861637120 |
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| author | Welkin H Pope Charles A Bowman Daniel A Russell Deborah Jacobs-Sera David J Asai Steven G Cresawn William R Jacobs Jr Roger W Hendrix Jeffrey G Lawrence Graham F Hatfull Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Phage Hunters Integrating Research and Education Mycobacterial Genetics Course |
| author_facet | Welkin H Pope Charles A Bowman Daniel A Russell Deborah Jacobs-Sera David J Asai Steven G Cresawn William R Jacobs Jr Roger W Hendrix Jeffrey G Lawrence Graham F Hatfull Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Phage Hunters Integrating Research and Education Mycobacterial Genetics Course |
| author_sort | Welkin H Pope |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:54:40Z |
| format | Article |
| id | doaj.art-3bc1b58b6d124a06a5de0dee6ee7b7f3 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:54:40Z |
| publishDate | 2015-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-3bc1b58b6d124a06a5de0dee6ee7b7f32022-12-22T02:05:05ZengeLife Sciences Publications LtdeLife2050-084X2015-04-01410.7554/eLife.06416Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversityWelkin H Pope0Charles A Bowman1Daniel A Russell2Deborah Jacobs-Sera3David J Asai4Steven G Cresawn5William R Jacobs Jr6Roger W Hendrix7Jeffrey G Lawrence8Graham F Hatfull9Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary SciencePhage Hunters Integrating Research and EducationMycobacterial Genetics CourseDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesHoward Hughes Medical Institute, Chevy Chase, United StatesDepartment of Biology, James Madison University, Harrisonburg, United StatesDepartment of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesDepartment of Biological Sciences, University of Pittsburgh, Pittsburgh, United StatesThe 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.https://elifesciences.org/articles/06416bacteriophagegenomicevolution |
| spellingShingle | Welkin H Pope Charles A Bowman Daniel A Russell Deborah Jacobs-Sera David J Asai Steven G Cresawn William R Jacobs Jr Roger W Hendrix Jeffrey G Lawrence Graham F Hatfull Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Phage Hunters Integrating Research and Education Mycobacterial Genetics Course Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity eLife bacteriophage genomic evolution |
| title | Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| title_full | Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| title_fullStr | Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| title_full_unstemmed | Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| title_short | Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| title_sort | whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity |
| topic | bacteriophage genomic evolution |
| url | https://elifesciences.org/articles/06416 |
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