Microevolutionary Genomics of Rhizobium etli .


Earlier genetic population studies pointed out that R. etli has high diversity levels as measured by multilocus enzyme electrophoresis. There are also differences in plasmid number and size. Recently, we obtain the complete genome sequence of R. etli CFN42. This strain contains six large plasmids and a circular chromosome that together account for 6, 530, 234 bp. In this context, we want to evaluate the levels of molecular variation among strains of R. etli, to answer the following questions:

  1. What is the amount of variation among the R. etli strains?
  2. Is there a difference among the rates of evolution of the different replicons of R. etli?
  3. Is the symbiotic plasmid (or any other replicon, set of genes, or genes) under positive selection?
  4. What is the main evolutive force that drives the diversification of R. etli? Is it the mutation or recombination?

Our approach consists on collect random sequences from the genome of 10 R. etli strains from distinct geographical origin to a depth of 0.5x. This will allow us to cover at least 60% of the genes determined for R. etli CFN42. By paired comparisons we will assess the amount of nucleotide polymorphisms (SNPs) between each strain in relation to the CFN42 strain. Several evolutionary models will be used to determine the rates of evolution and selection on replicons or individual genes.

To evaluate the role of recombination on the diversification of R. etli populations, we choose a local population already characterized by MLEE, and a set of polymorphic gene markers derived from the former experiment. These markers, located throughout the chromosome and the replicons of the CFN42 strain, will represent the ranges of variability high, medium or poor, found among geographically distant R. etli strains. Pairs of oligonucleotides for each marker will be designed and PCR products for 30 local strains will be raised and sequenced. Inferences on polymorphism degree and rates of recombination will be done by genetic population techniques (e. g. determination of heterocigocity and linkage disequilibrium).

Participants:

Dr. Víctor González, experimental design and analyses.
Biol. José L. Acosta, evaluation of recombination on local populations.
M. C. Rosa I. Santamaría, DNA sequencing and polymorphism analyses.
M. C. José L. Fernández, DNA sequencing.
Q. I. Patricia Bustos, polymorphism analyses.
M. C. Ismael L. Hernández, Bioinformatics.
Dr. Guillermo Dávila, data analysis.


Evolutionary Genomics Program