Diversification of DNA sequences in the symbiotic genome of Rhizobium etli

Margarita Flores, Lucia Morales, Agustín Avila, Víctor González, Patricia Bustos, Delfino García, Yolanda Mora, Xianwu Guo, Julio Collado-Vides, Daniel Piñero, Guillermo Dávila, Jaime Mora, Rafael Palacios

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification. Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Original languageAmerican English
Pages (from-to)7185-7192
Number of pages8
JournalJournal of Bacteriology
DOIs
StatePublished - 1 Nov 2005
Externally publishedYes

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Rhizobium etli
Plasmids
Nucleotides
Genome
Replicon
Rhizobium
Plant Roots
Phaseolus
Symbiosis
Microbiology
Islands
Genetic Recombination
Single Nucleotide Polymorphism
Nitrogen
Chromosomes
Bacteria
Mutation
DNA
Population
Genes

Cite this

Flores, M., Morales, L., Avila, A., González, V., Bustos, P., García, D., ... Palacios, R. (2005). Diversification of DNA sequences in the symbiotic genome of Rhizobium etli. Journal of Bacteriology, 7185-7192. https://doi.org/10.1128/JB.187.21.7185-7192.2005
Flores, Margarita ; Morales, Lucia ; Avila, Agustín ; González, Víctor ; Bustos, Patricia ; García, Delfino ; Mora, Yolanda ; Guo, Xianwu ; Collado-Vides, Julio ; Piñero, Daniel ; Dávila, Guillermo ; Mora, Jaime ; Palacios, Rafael. / Diversification of DNA sequences in the symbiotic genome of Rhizobium etli. In: Journal of Bacteriology. 2005 ; pp. 7185-7192.
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abstract = "Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification. Copyright {\circledC} 2005, American Society for Microbiology. All Rights Reserved.",
author = "Margarita Flores and Lucia Morales and Agust{\'i}n Avila and V{\'i}ctor Gonz{\'a}lez and Patricia Bustos and Delfino Garc{\'i}a and Yolanda Mora and Xianwu Guo and Julio Collado-Vides and Daniel Pi{\~n}ero and Guillermo D{\'a}vila and Jaime Mora and Rafael Palacios",
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Flores, M, Morales, L, Avila, A, González, V, Bustos, P, García, D, Mora, Y, Guo, X, Collado-Vides, J, Piñero, D, Dávila, G, Mora, J & Palacios, R 2005, 'Diversification of DNA sequences in the symbiotic genome of Rhizobium etli', Journal of Bacteriology, pp. 7185-7192. https://doi.org/10.1128/JB.187.21.7185-7192.2005

Diversification of DNA sequences in the symbiotic genome of Rhizobium etli. / Flores, Margarita; Morales, Lucia; Avila, Agustín; González, Víctor; Bustos, Patricia; García, Delfino; Mora, Yolanda; Guo, Xianwu; Collado-Vides, Julio; Piñero, Daniel; Dávila, Guillermo; Mora, Jaime; Palacios, Rafael.

In: Journal of Bacteriology, 01.11.2005, p. 7185-7192.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Diversification of DNA sequences in the symbiotic genome of Rhizobium etli

AU - Flores, Margarita

AU - Morales, Lucia

AU - Avila, Agustín

AU - González, Víctor

AU - Bustos, Patricia

AU - García, Delfino

AU - Mora, Yolanda

AU - Guo, Xianwu

AU - Collado-Vides, Julio

AU - Piñero, Daniel

AU - Dávila, Guillermo

AU - Mora, Jaime

AU - Palacios, Rafael

PY - 2005/11/1

Y1 - 2005/11/1

N2 - Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification. Copyright © 2005, American Society for Microbiology. All Rights Reserved.

AB - Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification. Copyright © 2005, American Society for Microbiology. All Rights Reserved.

U2 - 10.1128/JB.187.21.7185-7192.2005

DO - 10.1128/JB.187.21.7185-7192.2005

M3 - Article

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EP - 7192

JO - Journal of Bacteriology

JF - Journal of Bacteriology

SN - 0021-9193

ER -