Table_4_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.

本研究为开创性工作，首次针对豇豆（Vigna unguiculata）激酶的基因组与转录组数据开展分析。本研究系统评估了豇豆激酶组（kinome），涵盖其全基因组分布特征、基因与蛋白水平的结构特性、序列进化规律、绿色植物（Viridiplantae）物种间的保守性，以及3种不同胁迫条件下豇豆基因型中的基因表达情况；所涉胁迫包括生物胁迫（损伤后接种病毒——菜豆花叶病毒CABMV或豇豆斑驳病毒CPSMV）与非生物胁迫（根系脱水）。
豇豆激酶（VuPKs）的结构特征显示，1293个真正功能性的VuPKs可划分为20个类群与118个不同家族。其中类受体激酶-Pelle（RLK-Pelle）为最大类群，包含908个成员。针对VuPKs基因组扩张与跨Viridiplantae物种保守性的机制解析表明，分散复制与串联复制是塑造VuPKs基因组分布模式的主要驱动力；同时VuPKs与其他豆科物种具有较高的同源性指数与共线性（synteny）。Ka/Ks比值分析显示，91%的串联复制事件均处于纯化选择压力之下。
RLK-Pelle类家族启动子区域的候选顺式调控元件与多种转录因子（Transcription Factors，简称TFs）存在关联；其中C2H2型TFs与该类群中几乎所有被分析家族的启动子区域紧密相关。转录层面的分析结果表明，VuPKs的上调表达具有胁迫特异性、基因型特异性或组织特异性（或三者兼具）。在所有受试胁迫下上调表达最为显著的家族为RLK-Pelle_DLSV与CAMK_CAMKL-CHK1。
针对根系脱水胁迫的分析显示，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密切相关。此外，根系脱水条件下上调表达的VuPKs可能助力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VuPKs的进化机制与分子功能研究奠定了重要基础。