The genome of cowpea (<em>Vigna unguiculata</em> [L.] Walp.)
2019
Lonardi, Stefano | Muñoz-Amatriaín, María | Liang, Qihua | Shu, Shengqiang | Wanamaker, Steve I | Lo, Sassoum | Tanskanen, Jaakko | Schulman, Alan H | Zhu, Tingting | Luo, Ming-Cheng | Alhakami, Hind | Ounit, Rachid | Hasan, Abid Md | Verdier, Jérôme | Roberts, Philip A | Santos, Jansen Rp | Ndeve, Arsenio | Dolezel, Jaroslav | Vrána, Jan | Hokin, Samuel A | Farmer, Andrew D | Cannon, Steven B | Close, Timothy J | University of California [Riverside] (UC Riverside) ; University of California (UC) | United States Department of Energy | Natural Resources Institute Finland (LUKE) | University of California [Davis] (UC Davis) ; University of California (UC) | Institut de Recherche en Horticulture et Semences (IRHS) ; Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST | Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH) ; Faculty of Science [Univ Palacký] ; Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS) ; Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS) | National center for genome resources (NCGR) | USDA-ARS : Agricultural Research Service | NSF IOS-1543963 (“Advancing the Cowpea Genome for Food Security”), NSF IIS-1526742(“Algorithms for Genome Assembly of Ultra-Deep Sequencing Data”) and NSF IIS-1814359 (“Improving de novoGenome Assembly using Optical Maps”). Estimation of the genome size was supported by the Czech Ministry of Education, Youth and Sports (award LO1204 from the National Program of Sustainability I). The analysis of gene families was provided through by in-kind contributions from the USDA Agricultural Research Service, project 5030-21000-069-00-D, while the repetitive elements analysis was supported by the Academy of Finland “Papugeno” (Decision 298314).
International audience
Show more [+] Less [-]English. 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).
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