Diversity and genome dynamics of marine cyanophages using metagenomic analyses

Authors

  • Yingfei Ma,

    1. Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
    Current affiliation:
    1. Department of Medicine, New York University School of Medicine, New York, NY, USA
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    • Y.M. and L.Z.A. contributed equally to this work.
  • Lisa Zeigler Allen,

    1. Microbial and Environmental Genomics Department, J. Craig Venter Institute, San Diego, CA, USA
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    • Y.M. and L.Z.A. contributed equally to this work.
  • Brian Palenik

    Corresponding author
    1. Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
    • For correspondence. E-mail bpalenik@ucsd.edu; Tel. (+1) 858 534 7505; Fax (+1) 858 534 7313.

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Summary

Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches.

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