Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods Metadata

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Title

  • Main Title Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

Creator

  • Author: Wu, Liyou
    Creator Type: Personal
  • Author: Yi, T. Y.
    Creator Type: Personal
  • Author: Van Nostrand, Joy
    Creator Type: Personal
  • Author: Zhou, Jizhong
    Creator Type: Personal

Contributor

  • Sponsor: Physical Biosciences Division
    Contributor Type: Organization

Publisher

  • Name: Lawrence Berkeley National Laboratory
    Place of Publication: Berkeley, California
    Additional Info: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

Date

  • Creation: 2010-05-17

Language

  • English

Description

  • Content Description: Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.
  • Physical Description: 1

Subject

  • Keyword: Pacific Ocean
  • Keyword: Dna
  • STI Subject Categories: 59
  • Keyword: Columbia River
  • Keyword: Sediments
  • Keyword: Uranium
  • STI Subject Categories: 54
  • Keyword: Bioremediation
  • Keyword: Us Doe Phylogenetic Analyses, Shewanella, Doe Hanford Uranium Bioremediation Site
  • Keyword: Clostridium
  • Keyword: Nucleotides
  • Keyword: Baltic Sea
  • Keyword: Rhodopseudomonas
  • Keyword: Trees
  • Keyword: Strains
  • Keyword: Resolution
  • Keyword: Phylogenetic Analyses, Shewanella, Doe Hanford Uranium Bioremediation Site
  • Keyword: Hybridization
  • Keyword: Functionals
  • Keyword: Genes

Source

  • Conference: 110th General Meeting of the American Society for Microbiology, San Diego, CA

Collection

  • Name: Office of Scientific & Technical Information Technical Reports
    Code: OSTI

Institution

  • Name: UNT Libraries Government Documents Department
    Code: UNTGD

Resource Type

  • Report

Format

  • Text

Identifier

  • Report No.: LBNL-3880E-Poster
  • Grant Number: DE-AC02-05CH11231
  • DOI: 10.2172/986917
  • Office of Scientific & Technical Information Report Number: 986917
  • Archival Resource Key: ark:/67531/metadc1015185