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Pelagiphages in the Podoviridiae family integrate into host genomes

By Yanlin Zhao, Fang Qin, Rui Zhang, Stephen J. Giovannoni, Zefeng Zhang, Jing Sun, Sen Du, Christopher Rensing

Posted 07 Sep 2018
bioRxiv DOI: 10.1101/410191 (published DOI: 10.1111/1462-2920.14487)

The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here we report 11 new pelagiphages in the Podoviridae family. Comparative genomic analysis revealed that they are all closely related to previously reported pelagiphages HTVC011P and HTVC019P, in the HTVC019Pvirus genus. HTVC019Pvirus pelagiphages share a core genome of 15 genes, with a pan-genome of 234 genes. Phylogenomic analysis clustered these pelagiphages into four subgroups. Integrases were identified in all but one pelagiphage genome. Evidence of site-specific integration was obtained by high-throughput sequencing and sequencing PCR amplicons containing predicted integration sites, demonstrating the capacity of pelagiphages to propagate by both lytic and lysogenic infection. HTVC019P, HTVC021P, HTVC022P, HTVC201P and HTVC121P integrate into tRNA-Cys. HTVC011P, HTVC025P, HTVC105P, HTVC109P, HTVC119P and HTVC200P target tRNA-Leu, while HTVC120P integrates into tRNA-Arg. Evidence of pelagiphage integration was also retrieved from Global Ocean Survey database, suggesting the occurrence of pelagiphage integration in situ. The capacity of HTVC019Pvirus pelagiphages to integrate into host genomes suggests they could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction, and prophage-induced viral immunity. HTVC019Pvirus pelagiphages are a rare example of a lysogenic phage that can be implicated in ecological processes on broad scales, and thus have potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.

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