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

Abstract

SummaryCowpea (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.

Unequal contribution of two paralogous centromeric histones to function the cowpea centromere

“…Gene movements could be the result of double-strand break (DBS) repair through synthesis-dependent strand annealing mainly caused by transposable element activity (Wicker et al 2010). The class II transposons, which are the major group of classical cut-and-paste transposons, comprise 6.1% of the cowpea genome (Lonardi et al 2019). Chromosome synteny analysis between cowpea and its close relatives V. angularis, V. radiata and P. vulgaris revealed that chromosome 1 and 5 display rearrangements specific to the genus Vigna (Lonardi et al 2019).…”

“…The class II transposons, which are the major group of classical cut-and-paste transposons, comprise 6.1% of the cowpea genome (Lonardi et al 2019). Chromosome synteny analysis between cowpea and its close relatives V. angularis, V. radiata and P. vulgaris revealed that chromosome 1 and 5 display rearrangements specific to the genus Vigna (Lonardi et al 2019). In V. angularis and V. radiata , the ancestral CENH3 locus is conserved suggesting that CENH3 movement only occurred in some Vigna species during the rearrangement of chromosomes likely together with the activation of transposable elements.…”

“…CENH3 (Vigan.09G168600) (Sakai et al 2015; Sakai et al 2016) of Azuki bean ( Vigna angularis (Willd.) Ohwi & Ohashi) was used for the in silico identification of cowpea CENH3 in genomic and transcriptomic data of cowpea genotype IT97K-499-35 and IT86D-1010 (Spriggs et al 2018; Lonardi et al 2019). Trizol-isolated RNA from young leaves were used to generate cDNA with a cDNA synthesis kit (Thermo Scientific).…”

“…Transcript expression patterns for CENH3 genes were also analyzed using LCM-seq datasets based on laser captured microdissection of cowpea reproductive cells as described in (Gursanscky et al 2019). Reads were aligned against the V. unguiculata IT97K-499-35 genome using Biokanga as described (Spriggs et al 2018; Lonardi et al 2019) and uniquely aligned reads were counted for each gene.…”

“…Cowpea ( Vigna unguiculata (L.) Walp) belongs to the genus Vigna, comprising more than 200 species. Cowpea is diploid (2n = 2x = 22) with a genome size of 640.6 Mb (Lonardi et al 2019). Wild cowpea species are pantropically distributed with highest genetic diversity observed in South Africa, indicating this region is the site of origin (Padulosi and Ng 1997).…”