Draft genome sequence of a less-known wild Vigna: Beach pea (V. marina cv. ANBp-14-03)
Awnindra Kumar Singh,
A. Velmurugan,
Debjyoti Sen Gupta,
Jitendra Kumar,
Ravi Kesari,
Aravind Konda,
Narendra Pratap Singh,
Sibnarayan Dam Roy,
Utpal Biswas,
R. Rahul Kumar,
Sanjay Singh
Affiliations
Awnindra Kumar Singh
ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India; Division of Crop Improvement, ICAR - Indian Institute of Pulses Research, Kanpur 208024, Uttar Pradesh, India; Correspondence to: A.K. Singh, ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India.
A. Velmurugan
ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India
Debjyoti Sen Gupta
Division of Crop Improvement, ICAR - Indian Institute of Pulses Research, Kanpur 208024, Uttar Pradesh, India; Corresponding author.
Jitendra Kumar
Division of Crop Improvement, ICAR - Indian Institute of Pulses Research, Kanpur 208024, Uttar Pradesh, India
Ravi Kesari
Department of Plant Breeding and Genetics, Bhola Paswan Shastri Agricultural College, Purnea, Bihar 854302, India
Aravind Konda
Division of Plant Biotechnology, ICAR - Indian Institute of Pulses Research, Kanpur 208024, Uttar Pradesh, India
Narendra Pratap Singh
Division of Plant Biotechnology, ICAR - Indian Institute of Pulses Research, Kanpur 208024, Uttar Pradesh, India
Sibnarayan Dam Roy
ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India
Utpal Biswas
ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India
R. Rahul Kumar
ICAR-Central Island Agricultural Research Institute, Port Blair 744101, Andaman & Nicobar Islands, India
Sanjay Singh
ICAR - National Research Centre for Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
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. Keywords: Beach pea, Vigna marina, NextSeq 500, Whole-genome sequencing, Salinity tolerance
