Whole genome sequencing reveals transcriptional and translational elements potentially regulating biotic and abiotic stress responses in cowpea

Cowpea (Vigna unguiculata (L.) Walp.) is a highly versatile and resilient crop, globally ranking as the third most pivotal grain legume. However, various biotic, abiotic, and physiological challenges, often hinder its productivity. Cowpea exhibits complex environmental adaptive responses regulated at the transcriptional and translational levels through mechanisms such as resistance genes (R-genes), transcription-associated proteins (TAPs), and protein kinases (PKs). A comprehensive study was conducted based on a whole-genome hybrid assembly (Illumina and Nanopore) in cowpea, revealing the identification of 2188 R-genes (29 classes), 5573 TAPs (118 families) and 1135 PKs (22 groups, 122 families). Among the R-genes, Kinases (KIN) and transmembrane proteins (RLKs and RLPs) were prominent, while CCHC (Zn), C2H2, MYB-HB-like, WD40-like, bHLH, and ERF families were notable among TAPs. The largest kinome group, RLK-Pelle, encompassed over three-fifths of the cowpea PKs (VuPKs), followed by CAMK and CMGC groups. Two and three novel families in TAPs (ABTB and CW-ZN-B3_VAL) and PKs (RLK-Pelle-URK-1, RLK-Pelle-URK-2, TKL-Cr-3), respectively, were identified along with two novel PK groups (NAK and TLK). Dispersed and tandem duplication events under purifying selection mainly contributed to kinome expansion, with chromosome 'Vu03' anchoring the maximum PKs. This investigation delves into the biological intricacies with manipulative potential to enhance cowpeas' resilience to environmental challenges without compromising yield.