Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness Metadata

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Title

  • Main Title Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

Creator

  • Author: Wu, L.
    Creator Type: Personal
  • Author: Liu, X.
    Creator Type: Personal
  • Author: Fields, M.W.
    Creator Type: Personal
  • Author: Thompson, D.K.
    Creator Type: Personal
  • Author: Bagwell, C.E.
    Creator Type: Personal
  • Author: Tiedje, J. M.
    Creator Type: Personal
  • Author: Hazen, T.C.
    Creator Type: Personal
  • Author: Zhou, J.
    Creator Type: Personal

Contributor

  • Sponsor: Lawrence Berkeley National Laboratory. Earth Sciences 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: 2008-01-15

Language

  • English

Description

  • Content Description: The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

Subject

  • Keyword: Dna
  • Keyword: Microorganisms
  • Keyword: Genes
  • STI Subject Categories: 54
  • Keyword: Pseudomonas
  • STI Subject Categories: 58
  • Keyword: Hybridization
  • Keyword: Strains

Source

  • Journal Name: The ISME Journal; Journal Volume: 2; Related Information: Journal Publication Date: 2008

Collection

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

Institution

  • Name: UNT Libraries Government Documents Department
    Code: UNTGD

Resource Type

  • Article

Format

  • Text

Identifier

  • Report No.: LBNL-1126E
  • Grant Number: DE-AC02-05CH11231
  • DOI: 10.1038/ismej.2008.23
  • Office of Scientific & Technical Information Report Number: 941680
  • Archival Resource Key: ark:/67531/metadc899263