Stefano Lonardi1,*,‡ , Mar-ıa Mu noz-Amatria-ın2,*,†,‡ , Qihua Liang1, Shengqiang Shu3, Steve I. Wanamaker2, Sassoum
Lo2, Jaakko Tanskanen4,5,6, Alan H. Schulman4,5,6, Tingting Zhu7, Ming-Cheng Luo7, Hind Alhakami1, Rachid Ounit1,
Abid Md. Hasan1, Jerome Verdier8, Philip A. Roberts9, Jansen R.P. Santos9,10, Arsenio Ndeve9, Jaroslav Dole-zel11 ,
Jan Vr-ana11, Samuel A. Hokin12, Andrew D. Farmer12, Steven B. Cannon13 and Timothy J. Close2
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 singlehaplotype
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.
Keywords : chromosomal inversion, cowpea, domestication, genome annotation, genome evolution, genome size, next-generation sequencing, legumes, Phaseolus vulgaris, repetitive elements, Vigna unguiculata.
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