Table_8_The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses.XLSX

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.本研究为开创性探索，系首个针对豇豆（Vigna unguiculata，俗称 cowpea）激酶的基因组及转录组数据开展分析的工作。本研究对豇豆激酶组（kinome）进行了系统评估，涵盖其全基因组分布与结构特征（基因及蛋白层面）、序列进化规律、在绿色植物界（Viridiplantae）物种间的保守性，以及三种豇豆基因型在不同胁迫条件下的基因表达情况，胁迫类型包括生物胁迫（机械损伤后接种病毒——CABMV或CPSMV）与非生物胁迫（根系脱水）。豇豆蛋白激酶（VuPKs）的结构特征分析显示，1293个真实可信的VuPKs可划分为20个类群与118个不同家族，其中RLK-Pelle类群为最大类群，包含908个成员。针对VuPKs基因组扩张机制及其在绿色植物界物种间保守性的分析表明，散在重复与串联重复分别是塑造VuPKs分布模式的主要驱动力，而VuPKs与其他豆科物种则呈现出较高的同源性指数与共线性特征。Ka/Ks比率分析显示，近91%的串联重复事件处于纯化选择压力之下。RLK-Pelle类群基因启动子区域的候选顺式调控元件（cis-regulatory elements）与多种转录因子（TFs）存在关联，其中C2H2型转录因子与该类群几乎所有被检视的家族的启动子区域均呈现紧密关联。在转录层面，研究发现VuPKs的上调表达受胁迫类型、基因型或组织特异性调控（或为上述因素的组合效应）。在所有受试胁迫下均呈现上调响应的优势家族为RLK-Pelle_DLSV与CAMK_CAMKL-CHK1。针对根系脱水胁迫，研究显示上调表达的VuPKs与脱落酸（ABA）信号通路、生长素转运及钾离子代谢过程密切相关。此外，根系脱水胁迫下上调表达的VuPKs可能助力本研究中受试豇豆基因型的关键生理策略：在响应根系脱水的同时激活生物胁迫防御机制。本研究为后续针对VuPKs的进化与分子功能研究奠定了坚实基础。