Cowpea genome sequence (cultivar IT86D-1010)

This resource is a de novo genome assembly of the cowpea (Vigna unguiculata (L.) Walp) cultivar IT86D-1010. This cultivar has become the preferred germplasm for developing transgenic cowpea plants, either genetically modified or gene edited. For the production and characterization of genetically modified cowpeas, it is crucial to have a high-quality genomic sequence of the cultivar being transformed. Although there are publicly accessible genomic sequences for cowpea, the reference cultivar is IT97K-499-35 (Lonardi et al., 2019). There is also a previously published version of IT86D-1010 based on Illumina short reads (Spriggs, et al, 2018), however this is too fragmented. The submitted dataset is a new, high-quality, assembled genomic sequence for the cowpea cultivar IT86D-1010, using Oxford Nanopore Technology (ONT) long read sequencing, and corrected using the already published Illumina short reads (Spriggs, et al., 2018). The resulting genome consisted of 505 contigs, with a total assembly length of 537341206, and was comparable in quality to the IT97K-499-35 reference. Lineage: Plant material and tissue sample Cowpea (Vigna unguiculata) cultivar IT86D-1010 was originally sourced from the International Institute of Tropical Agriculture (IITA). Line have been maintained in CSIRO for more than 10 generations (not through single seed descent). Young unexpanded leaves were collected for DNA extraction. DNA Isolation and Sequencing For Illumina short read sequencing, DNA extraction was carried out using a Qiagen maxi DNA kit as per the manufacturer’s instructions. Illumina library preparation and sequencing of DNA was undertaken by the Australian Genome Research Facility (AGRF) with 2 × 100 bp standard insert paired-end sequencing using a Hiseq 2500 system, as described in Spriggs, et al. (2018), For Oxford Nanopore Technology (ONT) long read sequencing, DNA was isolated using the QIAGEN Genomic-tip as per the manufacturer’s instructions. DNA was extracted from a transformed IT86D-1010 line. Shorter DNA fragments (