title: Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA.|Present Address: Departments of Microbiology, Ohio State University, Columbus, OH, 43210, USA.
authors.forename: Ann C
authors.initials: AC
authors.lastname: Gregory
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.|Present Address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Solonenko
authors.affiliation: Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA.|Present Address: Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: J Cesar
authors.initials: JC
authors.lastname: Ignacio-Espinoza
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Copeland
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Sudek
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Maitland
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Chittick
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Filipa
authors.initials: F
authors.lastname: Dos Santos
authors.affiliation: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.|School of Physics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Weitz
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA.|Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.
authors.forename: Alexandra Z
authors.initials: AZ
authors.lastname: Worden
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA. mbsulli@gmail.com.|Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. mbsulli@gmail.com.|Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. mbsulli@gmail.com.|Present Address: Departments of Microbiology, Ohio State University, Columbus, OH, 43210, USA. mbsulli@gmail.com.|Present Address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA. mbsulli@gmail.com.|Present Address: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA. mbsulli@gmail.com.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
mesh_terms: D001435:Bacteriophages / Q000145:classification / Q000235:genetics*; D005075:Biological Evolution; D055028:Comparative Genomic Hybridization; D004247:DNA / Q000378:metabolism; D004279:DNA, Viral / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D008040:Genetic Linkage; D016679:Genome, Viral; D058507:Host Specificity; D056186:Metagenomics; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral; D004247:DNA
keywords: Bacteriophage; Cyanophage; Double-stranded DNA; Evolution; Phage; Species; Virus