Genome of Mesoamerican Common Bean - An Additional Resource for the Legume Genomics

Common bean (Phaseolus vulgaris) is important grain legume for the human nourishment; it is organized in two genetically differentiated gene pools - Andean and Mesoamerican. The genome of the Andean variant was recently published by Schmutz et al. Here we present the genome of Mesoamerican pool, line BAT93. Our assembly is 549.6 Mb, with an N50 of 430Kb, and 81% of the scaffolds anchored to the linkage groups; genotype by sequencing data from a set of 60 F5 lines of a BAT93/Jalo advanced intercross was used for a misassembly correction. For gene annotation we used a combination of ab-initio predictions together with RNA data obtained from multiple tissues from plants grown under optimal and stress conditions. In total, 28,520 protein-coding genes with 62,512 transcripts encode 50,582 unique proteins. In addition, we identified 2,717 small and 1,401 long ncRNA genes. The sequencing of 61 RNA samples from different organs (root, stem, leaf, flower, axial meristems and fruits) and developmental stages, was used to generate gene transcription atlas. Co-expression networks contain functional modules related to development and regulation of the plant. The P. vulgaris phylome, i.e. the complete collection of phylogenetic trees for each gene, was reconstructed by using 13 other plant genomes, including 4 legumes. These trees were employed to delineate orthology and paralogy relationship, as well as to identify taxa-specific genes. Genes specific to legumes were enriched for functions related to symbiosis with soil microorganisms, and pathogen response; and the largest group of genes specific to bean was characterized as putative receptors with extracellular domains.