Genomics and Evolution of Rhizobia

Abstract

In the first decade of the twenty-first century, people working on rhizobia had been very excited about the release of the complete genomes of model strains including Mesorhizobium loti MAFF303099 (reclassified as M. japonicum) (Kaneko et al. 2000), Sinorhizobium meliloti 1021 (Galibert et al. 2001), Bradyrhizobium japonicum USDA110 (reclassified as B. diazoefficiens) (Kaneko et al. 2002), Rhizobium etli CFN42 (Gonzalez et al. 2006), Rhizobium leguminosarum bv. viciae 3841 (Young et al. 2006), Bradyrhizobium sp. BTAi1 and ORS278 (Giraud et al. 2007), Azorhizobium caulinodans ORS571 (Lee et al. 2008), Cupriavidus taiwanensis LMG19424 (Amadou et al. 2008), Sinorhizobium sp. NGR234 (Schmeisser et al. 2009) and Sinorhizobium medicae WSM419 (Reeve et al. 2010). Notably, all of these genomes were sequenced using the Sanger platform, and these valuable earlier efforts have provided us essential information regarding general features of rhizobial genomes. For example, symbiosis genes are intensively clustered in a symbiosis island or a symbiosis plasmid, and genome organisation and gene content can vary drastically between different species. These features have been further validated by more than 100 complete rhizobial genomes obtained later on using next-generation sequencing platforms such as Illumina, Roche 454, Ion Torrent and PacBio. As shown in Fig. 4.1, there is a great variation in genome size of different strains/species within each genus, indicating diverse metabolic abilities of rhizobial germplasms.