Bian Xiuyan, Xie Tao, Chen Jiying, Li Chunxu, Yin Dandan, Zhang Wenbo
School of Tea and Coffee, Puer University, Puer, 665000, China.
State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
BMC Genomics. 2025 Jul 21;26(1):683. doi: 10.1186/s12864-025-11795-4.
Soil salinization is a common matter of concern all over the world, which severely affects plant production, soil health, and ecosystem stability. Birch is a significant afforestation tree species with great ecological, economic, and evolutionary value. It is an excellent model system for studying the acclimation and adaptation of woody plants to extreme environmental conditions due to the current advancements in genomics, genetic variability, and extensive studies with a focus on various biotic and abiotic stresses. To date, the genetic regulation of birch trees in defending against environmental stimuli, particularly salt stress, has made great progress. However, the information on how genes related to chloride ion (Cl) channels and transporters respond to salt stress remains poorly understood in birch.
Herein, we performed the genome-wide identification, evolutionary relationship, sequence analysis, and expression patterns of seven family genes encoding Cl channels or transporters in birch. We identified one, one, four, seven, 13, 56, and 67 genes belonging to the cation chloride co-transporter (CCC) family, bestrophin family, slow type anion channel (SLAC) family, chloride channel (CLC) family, aluminum-activated malate transporter (ALMT) family, nitrate transporter 1/peptide transporter family (NPF) family, and multidrug and toxic compound extrusion (MATE ) family, respectively. Except for motif prediction, a high similarity of the conserved domain composition, gene structures, and physicochemical properties was observed within each group of a certain gene family. Gene Ontology (GO) classification analysis showed that the genes encoding ALMTs, CCCs, CLCs, MATEs, NPFs, and SLACs were mainly involved in ion transport. Transcriptome profiles showed that there were 52 genes related to Cl transporters and channels differentially expressed in any tissue of the two birch species subjected to salt treatment. Of these, three genes, designated as BpCLCa/b, BpDTX45, and BpDTX18/19, were simultaneously expressed at altered levels in all tissues of the two birch species, which was consistent with the results of quantitative real-time polymerase chain reaction (RT-qPCR) assay. In addition, the molecular docking simulations showed that sodium ion (Na) and Cl, respectively, had a strong binding affinity towards BpCLCa/b, BpDTX45, and BpDTX18/19.
A total of 149 genes related to Cl channels and transporters were identified from the birch genome. We proposed BpCLCa/b, BpDTX45, and BpDTX18/19 as ion channels or transporters in controlling ionic homeostasis during salt stress response. The findings of our study can provide valuable resources for genetic improvement of salt-tolerant birch varieties for high-quality plantation forests in harsh environments.
土壤盐渍化是全球普遍关注的问题，严重影响植物生产、土壤健康和生态系统稳定性。桦树是一种具有重要生态、经济和进化价值的造林树种。由于基因组学、遗传变异性的当前进展以及针对各种生物和非生物胁迫的广泛研究，它是研究木本植物对极端环境条件的适应和驯化的优秀模型系统。迄今为止，桦树抵御环境刺激，特别是盐胁迫的遗传调控已取得很大进展。然而，关于氯离子（Cl）通道和转运蛋白相关基因如何响应盐胁迫的信息在桦树中仍知之甚少。
在此，我们对桦树中编码Cl通道或转运蛋白的七个家族基因进行了全基因组鉴定、进化关系、序列分析和表达模式研究。我们分别鉴定出属于阳离子氯离子共转运体（CCC）家族、Bestrophin家族、慢速型阴离子通道（SLAC）家族、氯离子通道（CLC）家族、铝激活苹果酸转运体（ALMT）家族、硝酸盐转运体1/肽转运体家族（NPF）家族和多药及有毒化合物外排（MATE）家族的1、1、4、7、13、56和67个基因。除基序预测外，在特定基因家族的每组基因中观察到保守结构域组成、基因结构和理化性质具有高度相似性。基因本体（GO）分类分析表明，编码ALMTs、CCCs、CLCs、MATEs、NPFs和SLACs的基因主要参与离子运输。转录组图谱显示，在经过盐处理的两种桦树的任何组织中，有52个与Cl转运蛋白和通道相关的基因差异表达。其中，三个基因，命名为BpCLCa/b、BpDTX45和BpDTX18/19，在两种桦树的所有组织中同时以改变的水平表达，这与定量实时聚合酶链反应（RT-qPCR）分析结果一致。此外，分子对接模拟表明，钠离子（Na）和Cl分别对BpCLCa/b、BpDTX45和BpDTX18/19具有很强的结合亲和力。
从桦树基因组中总共鉴定出149个与Cl通道和转运蛋白相关的基因。我们提出BpCLCa/b、BpDTX45和BpDTX18/19作为在盐胁迫响应过程中控制离子稳态的离子通道或转运蛋白。我们的研究结果可为在恶劣环境中高质量人工林耐盐桦树品种的遗传改良提供有价值的资源。
