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Plant J. 2019 Apr 24. doi: 10.1111/tpj.14349. [Epub ahead of print]

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

Author information

1
Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
2
Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
3
US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
4
Natural Resources Institute Finland (Luke), Helsinki, Finland.
5
Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
6
Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
7
Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
8
Institut de Recherche en Horticulture et Semences, INRA, Université d'Angers, 49071, Beaucouzé, France.
9
Department of Nematology, University of California, Riverside, CA, 92521, USA.
10
Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil.
11
Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic.
12
National Center for Genome Resources, Santa Fe, NM, 87505, USA.
13
US Department of Agriculture-Agricultural Research Service, Ames, Iowa, USA.

Abstract

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 to 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. This article is protected by copyright. All rights reserved.

KEYWORDS:

Phaseolus vulgaris ; Vigna unguiculata ; Chromosomal Inversion; Cowpea; Domestication; Genome Annotation; Genome Evolution; Genome Size; Legumes; Next-Generation Sequencing; Repetitive Elements

PMID:
31017340
DOI:
10.1111/tpj.14349

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