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PMID: 19363063 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences.

Applied and environmental microbiology ·Vol. 75 ·No. 11 ·2009-06-00 ·Pages 3634-40

Labonté JM, Reid KE, Suttle CA

Abstract

The distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb DNA polymerase (pol) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to the Strait of Georgia, British Columbia, Canada, and from the northeastern Gulf of Mexico. Restriction fragment length polymorphism analysis of 160 cloned PCR products revealed 29 distinct operational taxonomic units (OTUs), with OTUs within a site typically being more similar than those among sites. Phylogenetic analysis of the DNA pol gene fragments demonstrated high similarity between some environmental sequences and sequences from the marine podoviruses roseophage SIO1 and cyanophage P60, while others were not closely related to sequences from cultured phages. Interrogation of the CAMERA database for sequences from metagenomics data demonstrated that the amplified sequences were representative of the diversity of podovirus pol sequences found in marine samples. Our results indicate high genetic diversity within marine podovirus communities within a small geographic region and demonstrate that the diversity of environmental polymerase gene sequences for podoviruses is far more extensive than previously recognized.

MeSH Terms
British Columbia Cluster Analysis DNA Fingerprinting DNA Primers/genetics DNA, Viral/chemistry,genetics DNA-Directed DNA Polymerase/genetics Evolution, Molecular Geologic Sediments/virology Georgia Molecular Sequence Data Phylogeny Podoviridae/genetics Polymerase Chain Reaction/methods Polymorphism, Genetic Polymorphism, Restriction Fragment Length Seawater/virology Sequence Analysis, DNA Sequence Homology, Amino Acid Viral Proteins/genetics
Chemicals
DNA Primers DNA, Viral Viral Proteins DNA-Directed DNA Polymerase
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Labonté Jessica M
Departments of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
Reid Karen E
Suttle Curtis A
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
1098-5336
DOI
10.1128/AEM.02317-08
Published
2009-06-00
Epub
2009-00-10
Pages
3634-40
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC2687296
Subset
IM
Databases
GENBANK
AY258449, AY258450, AY258451, AY258452, AY258453, AY258454, AY258455, AY258456, AY258457, AY258458, AY258459, AY258460, AY258461, AY258463, AY258464, AY258465, AY258466
External Links
PubMed source DOI: 10.1128/AEM.02317-08 PMC Full Text View journal details
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