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

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, Jerome; Roberts, Philip A.; Santos, Jansen R. P.; Ndeve, Arsenio; Doležel, Jaroslav; Vrána, Jan; Hokin, Samuel A.; Farmer, Andrew D.; Cannon, Steven B.; Close, Timothy J.

doi:10.1111/tpj.14349

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

Journal Article · Mon Mar 25 00:00:00 EDT 2019 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.14349· OSTI ID:1625939

^[1]; ^[2]; Liang, Qihua ^[3]; Shu, Shengqiang ^[4]; Wanamaker, Steve I. ^[2]; Lo, Sassoum ^[2]; Tanskanen, Jaakko ^[5]; Schulman, Alan H. ^[5]; Zhu, Tingting ^[6]; Luo, Ming‐Cheng ^[6]; Alhakami, Hind ^[3]; Ounit, Rachid ^[3]; Hasan, Abid Md. ^[3]; Verdier, Jerome ^[7]; Roberts, Philip A. ^[8]; Santos, Jansen R. P. ^[9]; Ndeve, Arsenio ^[8]; ^[10]; Vrána, Jan ^[10]; Hokin, Samuel A. ^[11] more »

Department of Computer Science and Engineering University of California Riverside CA 92521 USA; DOE/OSTI
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
US Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
Natural Resources Institute Finland (Luke) Helsinki Finland; Institute of Biotechnology University of Helsinki Helsinki Finland; Viikki Plant Science Centre University of Helsinki Helsinki Finland
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
Department of Nematology University of California Riverside CA 92521 USA
Department of Nematology University of California Riverside CA 92521 USA; Departamento de Fitopatologia Instituto de Ciências Biológicas Universidade de Brasília Brasília DF Brazil
Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Olomouc Czech Republic
National Center for Genome Resources Santa Fe NM 87505 USA
US Department of Agriculture–Agricultural Research Service Ames IA USA

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Science Foundation; Czech Ministry of Education, Youth and Sports. Agricultural Research Service; Academy of Finland “Papugeno"

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625939

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 5 Vol. 98; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes Restrepo-Montoya, Daniel; Brueggeman, Robert; McClean, Phillip E. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-06844-z	journal	July 2020
A detached leaf assay for testing transient gene expression and gene editing in cowpea (Vigna unguiculata [L.] Walp.) Juranić, Martina; Nagahatenna, Dilrukshi S. K.; Salinas-Gamboa, Rigel Plant Methods, Vol. 16, Issue 1 https://doi.org/10.1186/s13007-020-00630-4	journal	June 2020
Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.) Herniter, Ira A.; Lo, Ryan; Muñoz-Amatriaín, María Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01346	journal	October 2019