TY - JOUR
T1 - Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination
AU - Acosta, José L.
AU - Eguiarte, Luis E.
AU - Santamaría, Rosa I.
AU - Bustos, Patricia
AU - Vinuesa, Pablo
AU - Martínez-Romero, Esperanza
AU - Dávila, Guillermo
AU - González, Víctor
N1 - Funding Information:
We thank José Espiritu, Ismael L Hernández, and José L Fernández for their help with technical and computational resources, and Miguel A Cevallos for critical reading of the manuscript. This work was supported by grants from CONACyT (CB131499 and U4633) and PAPIIT-UNAM (IN215908 and IN223005). JLA received a Ph. D. fellowship from CONACyT. We thank the Doctorate in Biomedical Sciences and specially to National Autonomous University of México. LEE contributed during a sabbatical visit to the University of California Irvine (UCI) in the laboratory of Brandon Gaut; this work was supported by UC-MEXUS, CONACYT, and DGAPA, UNAM.
PY - 2011
Y1 - 2011
N2 - Background: Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli. Results: We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity () was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low. Conclusion: Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.
AB - Background: Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli. Results: We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity () was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low. Conclusion: Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.
UR - http://www.scopus.com/inward/record.url?scp=80054057258&partnerID=8YFLogxK
U2 - 10.1186/1471-2148-11-305
DO - 10.1186/1471-2148-11-305
M3 - Artículo
C2 - 22004448
AN - SCOPUS:80054057258
SN - 1471-2148
VL - 11
JO - BMC Evolutionary Biology
JF - BMC Evolutionary Biology
IS - 1
M1 - 305
ER -