The genome of cowpea (Vigna unguiculata [L.] Walp.)

Authors: LONARDI, STEFANO - UNIVERSITY OF CALIFORNIA; MUNOZ-AMATRIAIN, MARIA - UNIVERSITY OF CALIFORNIA; LIANG, QIHUA - UNIVERSITY OF CALIFORNIA; SHU, SHENGQIANG - ENERGY JOINT GENOME INSTITUTE; WANAMAKER, STEVE - UNIVERSITY OF CALIFORNIA; LO, SASSOUM - UNIVERSITY OF CALIFORNIA; TANSKANEN, JAAKKO - UNIVERSITY OF HELSINKI; ZHU, TINGTING - UNIVERSITY OF CALIFORNIA; SCHULMAN, ALAN - UNIVERSITY OF HELSINKI; LUO, MING-CHENG - UNIVERSITY OF HELSINKI; ALHAKAMI, HIND - UNIVERSITY OF CALIFORNIA; OUNIT, RACHID - UNIVERSITY OF CALIFORNIA; ABID, HASAN - UNIVERSITY OF CALIFORNIA; VERDIER, JEROME - INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE (INRA); ROBERTS, PHILIP - UNIVERSITY OF CALIFORNIA; SANTOS, JANSEN - UNIVERSITY OF CALIFORNIA; NDEVE, ARSENIO - UNIVERSITY OF CALIFORNIA; DOLEZEL, JAROSLAV - INSTITUTE OF EXPERIMENTAL BOTANY; VRANA, JAN - INSTITUTE OF EXPERIMENTAL BOTANY; HOKIN, SAMUEL - NATIONAL CENTER FOR GENOME RESOURCES; FARMER, ANDREW - NATIONAL CENTER FOR GENOME RESOURCES; Cannon, Steven; CLOSE, TIMOTHY - UNIVERSITY OF CALIFORNIA

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2019
Publication Date: 4/24/2019
Citation: Lonardi, S., Munoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., Lo, S., Tanskanen, J., Zhu, T., Schulman, A.H., Luo, M., Alhakami, H., Ounit, R., Abid, H., Verdier, J., Roberts, P.A., Santos, J., Ndeve, A., Dolezel, J., Vrana, J., Hokin, S.A., Farmer, A.D., Cannon, S.B., Close, T.J. 2019. The genome of cowpea (Vigna unguiculata [L.] Walp.). Plant Journal. 98(5)767-782. https://doi.org/10.1111/tpj.14349.
DOI: https://doi.org/10.1111/tpj.14349

Interpretive Summary: A major objective for crop improvement for any species is to develop an accurate genome sequence - which can then be used as a detailed map to help identify genes and other genetic factors that control valuable traits. This study reports the first full genome sequence assembly for cowpea. Cowpea is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. Cowpea may also be an increasingly important crop worldwide, due to its tolerance to heat and drought, its protein-rich nutritional profile, and its ability (shared by most legume crops) to convert atmospheric nitrogen into a source of nitrogen fertilizer. This research identifies a large genomic change in a chromosomal region that is responsible for resistance to a parasitic plant (Striga or "witchweed") that is a serious problem in cowpea fields in Africa. The research also identifies a probable genetic factor that is responsible for the desirable traits of large seed and pod size in cowpea. This work will assist breeders and other scientists to more rapidly develop improved cowpea varieties, to benefit both small-holder farmers and consumers worldwide.

Technical Abstract: Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. A high-quality assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single molecule real-time sequencing, optical and genetic mapping, and a novel assembly reconciliation algorithm. A new estimate of the genome size, determined by flow cytometry is 641 Mb, of which 519 Mb is included in the assembled sequences and the remainder presumably is composed of long stretches of extremely repetitive sequences that are intractable for assembly. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes and there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared to other warm-season legumes that have been sequenced. A surprising outcome of this study is the identification of a chromosomal inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence also facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A new numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris).