Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

Hong Guo, Sheng Sun, Bertrand D. Eardly, Turlough Finan, Jianping Xu

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

Original languageEnglish (US)
Pages (from-to)862-875
Number of pages14
JournalGenome
Volume52
Issue number10
DOIs
StatePublished - Oct 1 2009

Fingerprint

Sinorhizobium meliloti
Open Reading Frames
Genome
Replicon
Genome Size
Chromosomes
Electrophoresis
Gels
Microbial Genome
Nitrogen-Fixing Bacteria
Genes
Bacteria

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Molecular Biology
  • Genetics

Cite this

Guo, Hong ; Sun, Sheng ; Eardly, Bertrand D. ; Finan, Turlough ; Xu, Jianping. / Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. In: Genome. 2009 ; Vol. 52, No. 10. pp. 862-875.
@article{cf19ccd3695043b3a3e26341a9004232,
title = "Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti",
abstract = "Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2{\%} of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7{\%} on pSymB and 3.7{\%} on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0{\%}, 16.5{\%}, and 15.3{\%} of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51{\%} to 6.35{\%}, and the percentage of ORFs that were duplicated ranged from 0.27{\%} to 8.56{\%}. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.",
author = "Hong Guo and Sheng Sun and Eardly, {Bertrand D.} and Turlough Finan and Jianping Xu",
year = "2009",
month = "10",
day = "1",
doi = "10.1139/G09-060",
language = "English (US)",
volume = "52",
pages = "862--875",
journal = "Genome",
issn = "0831-2796",
publisher = "National Research Council of Canada",
number = "10",

}

Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. / Guo, Hong; Sun, Sheng; Eardly, Bertrand D.; Finan, Turlough; Xu, Jianping.

In: Genome, Vol. 52, No. 10, 01.10.2009, p. 862-875.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

AU - Guo, Hong

AU - Sun, Sheng

AU - Eardly, Bertrand D.

AU - Finan, Turlough

AU - Xu, Jianping

PY - 2009/10/1

Y1 - 2009/10/1

N2 - Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

AB - Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

UR - http://www.scopus.com/inward/record.url?scp=70349799212&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349799212&partnerID=8YFLogxK

U2 - 10.1139/G09-060

DO - 10.1139/G09-060

M3 - Article

VL - 52

SP - 862

EP - 875

JO - Genome

JF - Genome

SN - 0831-2796

IS - 10

ER -