The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses

Abstract

The present work represents a pioneering effort, being the first to analyze genomic and transcriptomic data from Vigna unguiculata (cowpea) kinases. We evaluated the cowpea kinome considering its genome-wide distribution and structural characteristics (at the gene and protein levels), sequence evolution, conservation among Viridiplantae species, and gene expression in three cowpea genotypes under different stress situations, including biotic (injury followed by virus inoculation—CABMV or CPSMV) and abiotic (root dehydration). The structural features of cowpea kinases (VuPKs) indicated that 1,293 bona fide VuPKs covered 20 groups and 118 different families. The RLK-Pelle was the largest group, with 908 members. Insights on the mechanisms of VuPK genomic expansion and conservation among Viridiplantae species indicated dispersed and tandem duplications as major forces for VuPKs’ distribution pattern and high orthology indexes and synteny with other legume species, respectively. Ka/Ks ratios showed that almost all (91%) of the tandem duplication events were under purifying selection. Candidate cis-regulatory elements were associated with different transcription factors (TFs) in the promoter regions of the RLK-Pelle group. C2H2 TFs were closely associated with the promoter regions of almost all scrutinized families for the mentioned group. At the transcriptional level, it was suggested that VuPK up-regulation was stress, genotype, or tissue dependent (or a combination of them). The most prominent families in responding (up-regulation) to all the analyzed stresses were RLK-Pelle_DLSV and CAMK_CAMKL-CHK1. Concerning root dehydration, it was suggested that the up-regulated VuPKs are associated with ABA hormone signaling, auxin hormone transport, and potassium ion metabolism. Additionally, up-regulated VuPKs under root dehydration potentially assist in a critical physiological strategy of the studied cowpea genotype in this assay, with activation of defense mechanisms against biotic stress while responding to root dehydration. This study provides the foundation for further studies on the evolution and molecular function of VuPKs.

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

“…PKs have great importance in sensing the environment and its response at the gene-expression level. The results observed for cowpea (Ferreira-Neto et al, 2021) are similar to the results found in our study.…”

“…Regarding PK pIs, the results found for common bean were similar to those of other species, such as sorghum, sugarcane (Aono et al, 2021), grapevine (Zhu et al, 2018b), and especially cowpea (Ferreira-Neto et al, 2021). However, for molecular mass, considerable differences were observed.…”

“…Alike other species (Aono et al, 2021; Ferreira-Neto et al, 2021; Liu et al, 2015; Zhu et al, 2018a,b), the Pvu kinome presented a high percentage of PK gene pairs with a Ka/Ks ratio below 1, indicating that they are under purifying selection. This indicates that selection has acted to conserve the structure and stabilize the function of PKs along their evolutionary history.…”

“…Differently, in strawberry, of the 954 PKs analyzed, 920 presented two or more kinase domains and, therefore, 34 presented only one kinase domain (Liu et al, 2020). In cowpea only 6 PKs have only 1 kinase domain, while the rest have a higher number of kinases (Ferreira-Neto et al, 2021).…”

The Response of Cowpea (Vigna unguiculata) Plants to Three Abiotic Stresses Applied with Increasing Intensity: Hypoxia, Salinity, and Water Deficit

“…Several factors or mechanisms operate independently or jointly to enable plants to cope with abiotic stresses, especially under high salinity, drought, or water deficit; their tolerance is manifested as a complex trait [14]. Fine adaptation mechanisms of cowpea plants to stresses include the modulation of transcription factors determining cell proliferation [15] and upregulation of the members of kinase families [16]. These regulatory mechanisms induce anatomical, physiological, and biochemical adjustments of plants that are considered to be an integrated response of different organs, especially roots and leaves [17].…”