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. An 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 an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. 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; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an 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 facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Olomouc Czech Republic

Departamento de Fitopatologia Instituto de Ciências Biológicas Universidade de Brasília Brasília DF Brazil

Department of Botany and Plant Sciences University of California Riverside CA 92521 USA

Department of Computer Science and Engineering University of California Riverside CA 92521 USA

Department of Nematology University of California Riverside CA 92521 USA

Department of Plant Sciences University of California Davis CA 95616 USA

Institut de Recherche en Horticulture et Semences INRA Université d'Angers 49071 Beaucouzé France

Institute of Biotechnology University of Helsinki Helsinki Finland

National Center for Genome Resources Santa Fe NM 87505 USA

Natural Resources Institute Finland Helsinki Finland

US Department of Agriculture Agricultural Research Service Ames IA USA

US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA

Viikki Plant Science Centre University of Helsinki Helsinki Finland

Comment In

Plant J. 2019 Jun;98(5):765-766. doi: 10.1111/tpj.14382. PubMed

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