Comparative genomics of lupin rhizobial symbionts

Native bradyrhizobial symbionts of lupins thriving in the Iberian Peninsula were studied. The analysis included five species that preferred neutral or acid soils: L. angustifolius, L. luteus, L. hispanicus, L. micranthus and L. cosentinii, and the unique, recently described lupin species L. mariae-josephae, endemic of alkaline Chromic Luvisol soils (?terra rossa?) in Eastern Spain. Draft genome sequences of at least one strain from each lupin species were obtained by Illumina (PE, 2x300 bp, MySeq v. 3.0) sequencing, assembled with SPAdes, and annotated with the RAST server. Pairwise Average Nucleotide Identities (ANI) between genomes were calculated using JSpecies. The results showed a clear separation between strains nodulating L. mariae-josephae and those that nodulate lupins from acid soils. These results are in agreement with the observed host specificity, i. e. bradyrhizobia from L. mariae-josephae don?t nodulate most of the lupins from acid soils and any bradyrhizobia from acid soil lupins do nodulate, although inefficiently, L. mariae-josephae. In contrast, acid soil lupins are efficiently nodulated by bradyrhizobia isolated from any of these lupins. Consistent with this, comparison of symbiotic regions (nod, fix, nif genes), showed maximum differences between L. mariae-josephae strains and those from other lupins. Another genomic features were also compared and results will be discussed

Genomic analysis of three Bradyrhizobium geno(species) nodulating Lima bean (Phaseolus lunatus L.) in Peru

The Lima bean (Phaseolus lunatus), also known as pallar, ibes, garrofón or butter bean in Peru, México, Spain and USA, respectively, is the second most economically important species of Phaseolus. Peru is a centre of origin and domestication of Lima bean. This crop is cultivated mainly in the Central coast of Peru under a subtropical arid climate. In contrast to the common bean (Phaseolus vulgaris) which forms nodules with fast growing Rhizobium strains, the Lima bean forms nodules with slow growing bacteria of the Bradyrhizobium genus (López-López et al. 2013, Ormeño-Orrillo et al. 2006). We found strains of Bradyrhizobium yuanmingense and of three novel Bradyrhizobium genospecies inside P. lunatus nodules in Peru (Ormeño- Orrillo et al. 2006). Strains of the three novel genospecies were characterized by showing an extra-slow growing phenotype (generation time > 10 h-1) and strong alkali production in yeast extract mannitol medium. Two of the novel genospecies were recently named as Bradyrhizobium paxllaeri and Bradyrhizobium icense (Durán et al. 2014). B. paxllaeri strains dominate nodule occupancy followed by those of B. icense and then the third and yet-unnamed genospecies. With the aim to gain insights into this differential competitive ability, we sequenced the genome of one representative strain of each species. Sequencing was performed with the Illumina HiSeq or MiSeq platform and genome assembly with the SPAdes program. Gene prediction and automated annotation was performed with Prokka and RAST. Annotation of genes putatively involved in competitiveness was manually curated. Assemblies had from 55 to 175 contigs, with N50 sizes > 131 kb. Genome sizes of B. paxllaeri and B. icense were similar (8.2 Mb) and larger than that of the third genospecies (7.8 Mb). Preliminary analysis revealed differences between B. paxllaeri and the other two genospecies such as more genes for type IV pilus and two nodA genes. A comparative genomic analysis of P. lunatus symbionts will be presented at the meeting