November 20, 2018: Most content in the UA Campus Repository is not accessible using the search/browse functions due to a performance bug; we are actively working to resolve this issue. If you are looking for content you know is in the repository, but cannot get to it, please email us at email@example.com with your questions and we'll make sure to get the content to you.
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
AuthorGregory, Ann C.
Solonenko, Sergei A.
Ignacio-Espinoza, J. Cesar
dos Santos, Filipa
Weitz, Joshua S.
Worden, Alexandra Z.
Sullivan, Matthew B.
AffiliationUniv Arizona, Dept Soil Water & Environm Sci
Univ Arizona, Dept Ecol & Evolutionary Biol
Univ Arizona, Dept Mol & Cellular Biol
MetadataShow full item record
PublisherBIOMED CENTRAL LTD
CitationGenomic differentiation among wild cyanophages despite widespread horizontal gene transfer 2016, 17 (1) BMC Genomics
RightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at firstname.lastname@example.org.
AbstractBackground: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Results: Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra-and inter-lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Conclusions: These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.
NoteOpen Access Journal
VersionFinal published version
SponsorsOffice of Science of the U.S. Department of Energy (DOE) [DE-AC02-05CH11231]; Gordon and Betty Moore Foundation (GBMF) grants; Lucille and David Packard Foundation/MBARI [DOE DE-SC0004765, GBMF3788]; BIO5 [NSF OCE0940390]
- Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts.
- Authors: Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW
- Issue date: 2006 Jul
- Diversity and genome dynamics of marine cyanophages using metagenomic analyses.
- Authors: Ma Y, Allen LZ, Palenik B
- Issue date: 2014 Dec
- Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes.
- Authors: Ignacio-Espinoza JC, Sullivan MB
- Issue date: 2012 Aug
- Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges.
- Authors: Huang S, Wang K, Jiao N, Chen F
- Issue date: 2012 Feb
- Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B.
- Authors: Chénard C, Wirth JF, Suttle CA
- Issue date: 2016 Jun 14