Table_9_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.

本研究是一项开创性工作，首次对豇豆（Vigna unguiculata）激酶的基因组与转录组数据开展分析。我们从全基因组分布、基因及蛋白质水平的结构特征、序列进化、绿色植物（Viridiplantae）物种间的保守性，以及三种豇豆基因型在不同胁迫（包括生物胁迫：伤胁迫后接种病毒——菜豆花叶病毒CABMV或豇豆褪绿斑驳病毒CPSMV——以及非生物胁迫：根系脱水）下的基因表达情况等维度，对豇豆激酶组（kinome）进行了系统评估。豇豆激酶（VuPKs）的结构特征显示，1293个真实可信的VuPKs可划分为20个大类与118个不同的家族，其中类受体激酶-Pelle（RLK-Pelle）为最大类，包含908个成员。针对VuPK基因组扩张机制及绿色植物物种间保守性的分析表明，分散重复与串联重复是塑造VuPKs分布模式的主要驱动力，且VuPKs与其他豆科物种具有较高的同源性指数与共线性。Ka/Ks比值分析显示，91%的串联重复事件均处于纯化选择压力之下。类受体激酶-Pelle类家族的启动子区域中，预测存在与不同转录因子（TFs）结合的顺式调控元件，其中C2H2型转录因子与该类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显示，VuPKs的上调表达具有胁迫、基因型或组织特异性（或三者兼具）。在所有分析的胁迫处理中，上调表达最为显著的家族为RLK-Pelle_DLSV与CAMK_CAMKL-CHK1。关于根系脱水胁迫，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相关。此外，本试验中上调表达的VuPKs可帮助受试豇豆基因型激活关键生理策略：在响应根系脱水胁迫的同时，激活针对生物胁迫的防御机制。本研究为后续VuPKs的进化与分子功能研究奠定了坚实基础。