TY - JOUR T1 - The genome of cowpea (<em>Vigna unguiculata</em> [L.] Walp.) JF - bioRxiv DO - 10.1101/518969 SP - 518969 AU - Stefano Lonardi AU - María Muñoz-Amatriaín AU - Qihua Liang AU - Shengqiang Shu AU - Steve I. Wanamaker AU - Sassoum Lo AU - Jaakko Tanskanen AU - Alan H. Schulman AU - Tingting Zhu AU - Ming-Cheng Luo AU - Hind Alhakami AU - Rachid Ounit AU - Abid Md. Hasan AU - Jerome Verdier AU - Philip A. Roberts AU - Jansen R.P. Santos AU - Arsenio Ndeve AU - Jaroslav Doležel AU - Jan Vrána AU - Samuel A. Hokin AU - Andrew D. Farmer AU - Steven B. Cannon AU - Timothy J. Close Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/01/13/518969.abstract N2 - 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 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 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). ER -