Abedi Amin, Pourkarimi Daryakenari Mohadece, Zare Fatemeh, Allahi Somayeh, Hajiahmadi Zahra
Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
Agricultural Biotechnology Research Institute of Iran (ABRII), North Region Branch, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran.
Front Plant Sci. 2025 Jul 8;16:1506461. doi: 10.3389/fpls.2025.1506461. eCollection 2025.
Calcium (Ca) serves as a crucial intracellular messenger in plant signaling, particularly during stress responses. Precise regulation of calcium levels by transporters such as calcium/cation (CaCA) antiporters is essential for its effective function. However, the evolutionary dynamics and stress-related roles of the CaCA superfamily remain underexplored in key Brassicaceae crops. This study aimed to address this gap by investigating the hypothesis that genes in , , and have undergone distinct evolutionary trajectories influencing their roles in abiotic stress responses, using Arabidopsis thaliana for comparison. Using Hidden Markov Model (HMM) profiling, 93 genes were identified across these species. These genes were categorized into four phylogenetic clades: CAX, CCX, NCL, and MHX. Comprehensive analyses of their coding proteins physicochemical properties, subcellular localization, conserved motifs, and gene structures were performed. Codon usage bias (CUB) analysis showed CaCA genes have low codon bias and CUB indices indicated a complex interplay between mutational and selective pressures, highlighting the influence of natural selection and mutational biases in shaping these genes. Collinearity and duplication analyses highlighted the evolutionary dynamics of the CaCA gene family, with several segmental and whole-genome duplication (WGD) events contributing to their expansion. Notably, duplicated genes underwent negative selection pressure, which removed harmful mutations, resulting in slower evolution and maintaining the functional stability of CaCA genes throughout their evolutionary history. Analysis of regulatory elements (CREs) revealed their responsiveness to hormones and stresses, suggesting a potential role in plant environmental adaptation. Expression profiling of genes under abiotic stresses (dehydration, salinity, cold, and ABA) in was performed using publicly available RNA-seq datasets and analyzed with standard bioinformatics tools. Based on the results of expression analysis, key genes, such as , , , , , , , and , which are differentially expressed and potentially crucial for stress tolerance. This comprehensive study elucidates the evolutionary architecture of the gene family in Brassicaceae and identifies key genes potentially crucial for abiotic stress tolerance, thus offering a foundation for future functional studies aimed at improving crop resilience.
钙（Ca）在植物信号传导中作为关键的细胞内信使，尤其是在应激反应期间。通过钙/阳离子（CaCA）反向转运蛋白等转运体精确调节钙水平对其有效功能至关重要。然而，CaCA超家族在关键十字花科作物中的进化动态和与应激相关的作用仍未得到充分研究。本研究旨在通过研究以下假设来填补这一空白：与拟南芥相比，、和中的基因经历了不同的进化轨迹，影响它们在非生物应激反应中的作用。使用隐马尔可夫模型（HMM）分析，在这些物种中鉴定出93个基因。这些基因被分为四个系统发育分支：CAX、CCX、NCL和MHX。对它们编码蛋白质的理化性质、亚细胞定位、保守基序和基因结构进行了综合分析。密码子使用偏好（CUB）分析表明CaCA基因的密码子偏好较低，CUB指数表明突变压力和选择压力之间存在复杂的相互作用，突出了自然选择和突变偏好对这些基因形成的影响。共线性和重复分析突出了CaCA基因家族的进化动态，几个片段和全基因组重复（WGD）事件促成了它们的扩展。值得注意的是，重复基因经历了负选择压力，消除了有害突变，导致进化较慢，并在整个进化历史中维持了CaCA基因的功能稳定性。调控元件（CRE）分析揭示了它们对激素和应激的反应，表明其在植物环境适应中的潜在作用。利用公开可用的RNA-seq数据集对拟南芥中基因在非生物胁迫（脱水、盐度、寒冷和脱落酸）下的表达谱进行了分析，并使用标准生物信息学工具进行了分析。基于表达分析结果，关键基因如、、、、、、和差异表达，可能对胁迫耐受性至关重要。这项全面的研究阐明了十字花科基因家族的进化结构，并鉴定出对非生物胁迫耐受性可能至关重要的关键基因，从而为未来旨在提高作物抗逆性的功能研究提供了基础。
