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

Description

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.

Resources

Name Format Description Link
21 Sequence alignments between the reference genome sequence (in red) and available WGS scaffolds from parental accessions in the 10 genetic maps. The "orientation type" information is based on the haplotype comparisons in Data S3 and it is confirmed by sequence alignments in column F. https://data.usaid.gov/d/dxht-2exi
21 Cowpea gene models contained within the inversion region. https://data.usaid.gov/d/qe7i-iaxf
21 Polynomial formulae for each cowpea chromosome. The valid range of the polynomial is indicated by the start and end positions in columns B and C, the order of the best fit (from 7th to 11th) in column D, the full formula in column E, and the constants at three significant digits in columns F through Q. https://data.usaid.gov/d/xee6-zq8j
21 iSelect SNP information (Forward Strand) of IT97K-499-35 (Reference Genome) and parents in 10 genetic maps for SNPs on Vu03. https://data.usaid.gov/d/kfxm-kmpq
21 Gene counts per species in legume gene families, and loss/gain analysis for selected gene superfamilies. Enrichment p-values calculated using one-side Fisher's test for cowpea against each species individually, then averaged for each family across all comparisons. Species abbreviations are constructed from the first three letters of the genus and the first two of the species epithet, e.g. "glyma" = GLYcine MAx. See Table S11 for explicit species abbreviations and data sources. https://data.usaid.gov/d/ukb2-p2sg
21 iSelect SNP data of IT97K-499-35 when exported from the Genome Studio software as Forward Strand and when referring to the orientation of the SNP design sequence within the pseudochromosome sequences. https://data.usaid.gov/d/gd32-auq5
21 Insertion (INS) and deletion (DEL) variations identified by BreakDancer (Chen et al. 2009) in a set of 36 diverse cowpea accessions. Columns 2 -4 and 5-7 specify the coordinates of the two breakpoints. The orientation is a string that records the number of reads mapped to the (+) or (-) strand in the anchoring regions. The confidence score associated with the prediction is also shown. https://data.usaid.gov/d/2rm6-zbwh
21 Position of SNPs previously described (Muñoz-Amatriaín et al. 2017) from alignment of discovered by WGS sequencing of 36 accessions, 5 in the cowpea reference genome sequence. Information on SNPs included in the previous Illumina Cowpea iSelect Consortium Array genotyping platforms is also shown, including the alleles when exported from the Genome Studio software as Forward Strand. https://data.usaid.gov/d/44cx-8wbh

Tags

  • feed-the-future
  • nutritional-security
  • agriculture
  • snp-genotyping
  • innovation-lab
  • genome-sequence
  • cowpea
  • resilience
  • synteny
  • genetic-mapping
  • food-security

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