Assembly of Eleven Pseudomolecules Representing the Cowpea Genome Sequence

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the world. Despite its relevance to food security, actual yields of cowpea are much lower than the known yield potential and cowpea genome resources have lagged behind other major crop plants.

Here we report the first high-quality sequence of the cowpea genome (~620Mb estimated size), from IT97K-499-35. Using Single Molecule Real-Time Sequencing (Pacific Biosciences) ~6M reads were generated for a total of 56.8Gbp (~91x genome equivalent), with a read N50 of ~14.5Kbp. We obtained an assembly of 505Mbp using CANU, with contig N50 of ~5.3Mbp, contig L50 of 27 and the longest contig of ~18.4Mbp. We polished the draft assembly using Pacific Biosciences’ Quiver pipeline in SMRT Portal, then evaluated the quality and completeness using several independent metrics, including Illumina reads. We generated super-scaffolds by mapping the polished assembly onto a BioNano genome (BNG) optical map. The BNG map consisted of 508 contigs for a total length of ~622Mbp, and a N50 of ~1.6Mbp. The super-scaffold N50 was ~12Mbp, with the longest scaffold of ~30Mbps. Finally, we produced pseudomolecules by anchoring and orienting super-scaffolds to five genetic maps including 37,372 unique SNPs. We obtained eleven pseudomolecules for a total of 474Mbp. Cowpea pseudomolecule sequences will be available from http://www.int-cowpea.org/. Project was supported by the NSF BREAD program.