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Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli.

Authors
  • González, Víctor
  • Acosta, José L
  • Santamaría, Rosa I
  • Bustos, Patricia
  • Fernández, José L
  • Hernández González, Ismael L
  • Díaz, Rafael
  • Flores, Margarita
  • Palacios, Rafael
  • Mora, Jaime
  • Dávila, Guillermo
Type
Published Article
Journal
Applied and Environmental Microbiology
Publisher
American Society for Microbiology
Publication Date
Mar 01, 2010
Volume
76
Issue
5
Pages
1604–1614
Identifiers
DOI: 10.1128/AEM.02039-09
PMID: 20048063
Source
Medline
License
Unknown

Abstract

Strains of the same bacterial species often show considerable genomic variation. To examine the extent of such variation in Rhizobium etli, the complete genome sequence of R. etli CIAT652 and the partial genomic sequences of six additional R. etli strains having different geographical origins were determined. The sequences were compared with each other and with the previously reported genome sequence of R. etli CFN42. DNA sequences common to all strains constituted the greater part of these genomes and were localized in both the chromosome and large plasmids. About 700 to 1,000 kb of DNA that did not match sequences of the complete genomes of strains CIAT652 and CFN42 was unique to each R. etli strain. These sequences were distributed throughout the chromosome as individual genes or chromosomal islands and in plasmids, and they encoded accessory functions, such as transport of sugars and amino acids, or secondary metabolism; they also included mobile elements and hypothetical genes. Sequences corresponding to symbiotic plasmids showed high levels of nucleotide identity (about 98 to 99%), whereas chromosomal sequences and the sequences with matches to other plasmids showed lower levels of identity (on average, about 90 to 95%). We concluded that R. etli has a pangenomic structure with a core genome composed of both chromosomal and plasmid sequences, including a highly conserved symbiotic plasmid, despite the overall genomic divergence.

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