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

José Ribamar Costa Ferreira-Neto; Artemisa Nazaré da Costa Borges; Manassés Daniel da Silva; David Anderson de Lima Morais; João Pacífico Bezerra-Neto; Guillaume Bourque; Ederson Akio Kido; Ana Maria Benko-Iseppon

doi:10.3389/fpls.2021.667013

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

Front Plant Sci. 2021 Jun 14:12:667013. doi: 10.3389/fpls.2021.667013. eCollection 2021.

Authors

José Ribamar Costa Ferreira-Neto¹, Artemisa Nazaré da Costa Borges², Manassés Daniel da Silva¹, David Anderson de Lima Morais³, João Pacífico Bezerra-Neto², Guillaume Bourque⁴, Ederson Akio Kido¹, Ana Maria Benko-Iseppon²

Affiliations

¹ Laboratory of Molecular Genetics, Genetics Department, Federal University of Pernambuco, Recife, Brazil.
² Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil.
³ Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC, Canada.
⁴ Génome Québec Innovation Centre, McGill University, Montréal, QC, Canada.

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. K _a /K _s 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.

Keywords: kinase; mechanical injury; plants; root dehydration; virus.