Genome Divergence between Vigna angularis & Vigna nakashimae

Abstract

The Azuki bean, Vigna angularis (2n=2x=22), is one of the important legume crop grown in the world. Comparing the genome of domesticated (Vigna angularis) and undomesticated (Vigna nakashimae) forms of Azuki bean can facilitate crop improvement. We used the Next-generation massively parallel DNA sequencing technologies which provide ultrahigh throughput at a substantially lower unit data cost. However, the data generated is very short read length sequences and constructing de novo assembly from it is extremely challenging. Here, we describe a novel method for finding genome divergence between the domesticated and the wild variety of Azuki bean. We de novo sequenced and assembled the Vigna angularis and Vigna nakashimae genome, achieving an N50 contig size of approximately 11 and 7 kilo base pairs (kbp) respectively. The genome size of Azuki bean is estimated to be around 545 mega-bases (Mb). We predicted 45,985 protein-coding genes in Vigna angularis, 70% more than that of Arabidopsis, approximately similar to poplar and soybean. For Vigna nakashimae we predicted 38,965 protein-coding genes which is 40% more than Arabidopsis and approximately similar to potato. Vigna angularis diverged from Vigna nakashimae approximately 1.9 million years ago. The data obtained from structural translocations and gene categories from the evolutionary relationship between Vigna angularis and Vigna nakashimae suggest that these genes can be a probable cause for the domestication of Azuki bean. The development of this de novo short read assembly method creates new opportunities for building reference genome and carrying out accurate analyses of unexplored genomes in a cost effective manner as well as overcomes the limitations of the re-sequencing method for discovering structural translocations.