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Genomic analysis of multiple Roseophage SIO1 strains

Authors

  • Florent Angly,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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  • Merry Youle,

    1. Rainbow Rock, Ocean View, HI, USA.
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  • Bahador Nosrat,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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  • Shailaja Srinagesh,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
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  • Beltran Rodriguez-Brito,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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  • Patrick McNairnie,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. Computational Science Research Center, San Diego State University, San Diego, CA, USA.
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  • Gordafaried Deyanat-Yazdi,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
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  • Mya Breitbart,

    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. College of Marine Sciences, University of South Florida, St. Petersburg, FL, USA.
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  • Forest Rohwer

    Corresponding author
    1. Department of Biology, San Diego State University, San Diego, CA, USA.
    2. Center for Microbial Sciences, San Diego State University, San Diego, CA, USA.
      *E-mail forest@sunstroke.sdsu.edu; Tel. (+1) 619 594 1336; Fax (+1) 619 594 567.
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*E-mail forest@sunstroke.sdsu.edu; Tel. (+1) 619 594 1336; Fax (+1) 619 594 567.

Summary

Roseophage SIO1 is a lytic marine phage that infects Roseobacter SIO67, a member of the Roseobacter clade of near-shore alphaproteobacteria. Roseophage SIO1 was first isolated in 1989 and sequenced in 2000. We have re-sequenced and re-annotated the original isolate. Our current annotation could only assign functions to seven additional open reading frames, indicating that, despite the advances in bioinformatics tools and increased genomic resources, we are still far from being able to translate phage genomic sequences into biological functions. In 2001, we isolated four new strains of Roseophage SIO1 from California near-shore locations. The genomes of all four were sequenced and compared against the original Roseophage SIO1 isolated in 1989. A high degree of conservation was evident across all five genomes; comparisons at the nucleotide level yielded an average 97% identity. The observed differences were clustered in protein-encoding regions and were mostly synonymous. The one strain that was found to possess an expanded host range also showed notable changes in putative tail protein-coding regions. Despite the possibly rapid evolution of phage and the mostly uncharacterized diversity found in viral metagenomic data sets, these findings indicate that viral genomes such as the genome of SIO1-like Roseophages can be stably maintained over ecologically significant time and distance (i.e. over a decade and ∼50 km).

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