Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

Abstract

BackgroundGenetic 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.ResultsHere 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3286-x) contains supplementary material, which is available to authorized users.

Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors

“…; Gregory et al . ) is generally consistent with the plausibility of KTW dynamics, but observations of complex, natural communities that may support or refute this model are sparse or non‐existent.…”

“…; Gregory et al . ), so viruses likely have some impact at the broader ecotype or genus level. Similarly, the discovery of a new family of viruses ( Autolykiviridae ) with broad inter‐species host ranges (Kauffman et al .…”

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

“…Determination of fitness-conferring infection traits for the large collections of closely related phages (e.g., Pope et al, 2015; Gregory et al, 2016; Marston and Martiny, 2016) is a valuable metric that—while labor intensive to collect—would further test this OTU-defining model and enable the application of theory to advance viral community ecology.…”

“…These combined trait-based and comparative genomics analyses allowed us to test the validity of proposed sequence-based virus population delineations described above (Brum et al, 2015; Gregory et al, 2016). To do so, we considered Pseudoalteromonas hosts as viral niches and measured infection traits indicative of viral fitness in each niche.…”

Biological species in the viral world

“…We recently introduced a methodology that uses genome sequences to delineate reproductively isolated groups within bacteria and archaea based on their barriers of gene exchange, thereby offering a single framework to define biological species for any set of recombining organisms (21). Similarly, viruses do not rely on sexual reproduction; however, recent analyses of homologous recombination and network reconstructions suggest that species delineation based on gene flow would be possible for bacteriophages infecting cyanobacteria (22)(23)(24)(25)(26). Moreover, an experimental evolution study has shown that the mechanisms of…”