Genomic Characterization of Plant-Selected Microsymbionts in the Fabeae Legume Tribe: The Pangenome of Rhizobium leguminosarum bv. viciae

Members of the legume tribe Fabeae (Pisum, Lens, Lathyrus and Vicia) establish an effective root-nodule symbiosis with the bacterium Rhizobium leguminosarum bv viciae (Rlv). Previous studies have suggested that, given a choice, different Fabeae select specific genotypes of rhizobia from those available in the soil.

We have performed a Pool-Seq analysis from Rlv isolates obtained from pea, lentil, fava-bean and vetch nodules to show that plant-selected sub-populations are different at the single nucleotide polymorphism (SNP) level.

The genomes of individual bacterial isolates from each sub-population (9, 14, 9, and 9 from fava-bean, pea, vetch, and lentil, respectively) were sequenced at draft level (MiSeq v. 2, ca. 30x, 90 contigs) and analyzed (J-species, CMG-Biotools). All the isolates had similar genome sizes (≈7.5 Mb) and gene numbers (≈7,300). Each plant-selected subpopulation showed a closed pangenome and core genomes of similar size (≈11,500 and ≈4,800 genes, respectively). The addition of all four sub-population results in a larger, closed pangenome of 19,040 genes and a core genome of similar size (4,392 genes). Each sub-population contains a characteristic set of genes but no universal, plant-specific genes were found. The core genome obtained from all four sub-populations is probably a representative core genome for Rhizobium leguminosarum, given that the reference genome (Rhizobium leguminosarum bv. viciae strain 3841) contains most of the core genome. We have also analyzed the symbiotic cluster (nod), and different nod cluster genotypes were found in each sub-population.

Supported by MINECO (Consolider-Ingenio 2010, MICROGEN Project, CSD2009-00006).