Single Molecule, Real-Time Sequencing of the Genomes of Genus Vigna

Genus Vigna consists of legume crops such as azuki bean as well as about 100 wild species. A number of the wild species show the great adaptability to severe environmental conditions including high salt, acid or alkaline soil, and drought. Genome information is of great importance to promote researches to figure out how they adapted to the stress environments. As a first step to establish the genome basis of the genus Vigna, we sequenced the genome of azuki bean (V. angularis) using PacBio RSII platform. Given the 51x coverage data of the estimated 540Mbp genome size, errors in the raw PacBio reads were corrected by Sprai. We carried out de novo assembly using Celera Assembler, followed by polishing the contigs using Quiver. The final assembly consisted of 4,568 contigs spanning 523.4Mbp. The PacBio assembly was 15.3% larger than another assembly derived from Roche and Illumina sequences, suggesting that more repetitive regions were successfully assembled in the PacBio assembly. In order to anchor the PacBio contigs on the azuki’s 11 chromosomes, we conducted whole genome genotyping of the 1,000 F₂ individuals of azuki and its close relative using 6,000 SNP markers. In total 86% of the assembly were anchored by the 4,828 markers. Currently genome sequencing of the nine wild species is ongoing using PacBio RSII platform. In addition, another five wild species have been sequenced by Illumina platform. All the data including the genome sequences and gene annotation will be released from our Vigna genome database (Vigna Genome Server, ‘VigGS’).