Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations

TY - JOUR

T1 - Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations

AU - Lozano, Luis

AU - Hernandez-Gonzalez, Ismael

AU - Bustos, Patricia

AU - Santamaria, Rosa I.

AU - Souza, Valeria

AU - Young, J. Peter W.

AU - Davila, Guillermo

AU - Gonzalez, Victor

N1 - © 2009 American Society for Microbiology. This is an author produced version of a paper published in APPLIED AND ENVIRONMENTAL MICROBIOLOGY. Uploaded in accordance with the publisher's self archiving policy.

PY - 2010/10

Y1 - 2010/10

N2 - Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of Rhizobium etli CFN42 in a collection of 87 Rhizobium strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in R. etli CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (glyA and dnaB) and three symbiotic sequences (nodC and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the R. etli populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion.

AB - Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of Rhizobium etli CFN42 in a collection of 87 Rhizobium strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in R. etli CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (glyA and dnaB) and three symbiotic sequences (nodC and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the R. etli populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion.

KW - MESORHIZOBIUM-LOTI

KW - TRANSPOSABLE ELEMENTS

KW - DNA-SEQUENCES

KW - GENOME

KW - RECOMBINATION

KW - BACTERIA

KW - ISLAND

KW - DIVERSIFICATION

KW - SUBSTITUTION

KW - DIVERSITY

UR - http://www.scopus.com/inward/record.url?scp=78049295691&partnerID=8YFLogxK

U2 - 10.1128/AEM.01001-10

DO - 10.1128/AEM.01001-10

M3 - Article

SN - 0099-2240

VL - 76

SP - 6504

EP - 6513

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

IS - 19

ER -