Draft genome sequence of a less-known wild Vigna: Beach pea (V. marina cv. ANBp-14-03)

Abstract

Beach pea or beach cowpea (Vigna marina (Burm.) Merr.) belongs to the family Fabaceae. It is a close relative of cultivated Vigna species such as adzuki bean (V. angularis), cowpea (V. unguiculata), mung bean (V. radiata), and blackgram (V. mungo), and is distributed throughout the tropics. With its ability to tolerate salt stress, beach pea has great potential to contribute salt-tolerance genes for developing salt-tolerant cultivars in cultivated Vigna species. However, it is still underutilized in Vigna breeding programs. A draft genome sequence of beach pea was generated using a high-throughput next-generation sequencing platform, yielding 23.7 Gb of sequence from 79,929,868 filtered reads. A de novo genome assembly containing 68,731 scaffolds gave an N50 length of 10,272 bp and the assembled sequences totaled 365.6 Mb. A total of 35,448 SSRs, including 3574 compound SSRs, were identified and primer pairs for most of these SSRs were designed. Genome analysis identified 50,670 genes with mean coding sequence length 1042 bp. Phylogenetic analysis revealed highest sequence similarity with V. angularis, followed by V. radiata. Comparison with the V. angularis genome revealed 16,699 SNPs and 2253 InDels and comparison with the V. radiata genome revealed 17,538 SNPs and 2300 InDels. To our knowledge this is the first draft genome sequence of beach pea derived from an accession (ANBp-14-03) adapted locally in the Andaman and Nicobar Islands of India. The draft genome sequence may facilitate the genetic enhancement in cultivated Vigna species.