The genome-wide identification and adaptive evolution of slc9 genes in Leuciscus waleckii under extremely alkaline conditions
The genome-wide identification and adaptive evolution of slc9 genes in Leuciscus waleckii under extremely alkaline conditions
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极碱性条件下瓦氏雅罗鱼slc9基因的全基因组鉴定及适应性进化
DOI：
10.1016/j.gene.2022.146769
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发表时间：
2022
期刊：
影响因子：
3.5
通讯作者：
Xu Peng
中科院分区：
文献类型：
--
作者：
Yang Junyi;Zhou Zhixiong;Pu Fei;Zhou Tao;Xu Peng
·在瓦氏钩端螺旋体染色体基因组中共鉴定出11个slc9基因。·某些slc9基因在淡水和碱水种群中的表达存在显著差异。·SLC9基因编码蛋白在两个群体之间存在分子差异。·碱性群体中slc9基因的保守序列表明严格的自然选择。溶质载体家族9(Slc9)基因，特别是slc9a亚型编码蛋白，参与了H+在质膜和细胞膜上的电子中和逆向转运，细胞内pH和细胞体积的调节，以及系统水平上的电解质、酸碱和液体体积的平衡。这些功能特性决定了生物体挑战压力条件的潜在基础。然而，这些做得很好的研究更多地在哺乳动物身上报道。因此，在本研究中，从最新版本的瓦氏鲤鱼基因组中共鉴定出11个slc9基因，这是一种耐受极端碱性环境(pH 9.6)的鲤科鱼类。通过拷贝数、基因结构、基序组成、染色体定位和系统发育关系的分析，揭示了slc9基因的进化足迹。更重要的是，通过对采用重测序技术的淡水和碱水种群进行比较，在slc9a3.2基因的编码区有两个SNPs位于5‘UTR区和三个非同义突变。SLC9a3.2基因在极端碱性压力下的鳃组织中低表达。总体上讲，白纹伊蚊slc9基因家族是高度保守的。在淡水和碱水种群之间发生非同义突变的地方，发现了几个重要的高Fst值的SNPs，它们可能在特定的功能分化中发挥重要作用。SLC9基因具有明显的组织表达偏好，参与非生物胁迫反应，表明其具有生理功能和较强的自我调节能力。我们对极端条件下个体基因发生的遗传变异的洞察可以为基于不断增加的环境压力的基因组数据研究特定的分子机制提供一个可行的例子。
• A total of 11 slc9 genes were identified in the chromosome-level genome of L. waleckii. • The expression of certain slc9 genes is significantly different between freshwater and alkali water populations. • Molecular differences were found in slc9 gene coding proteins between two populations. • Conserved sequences of slc9 genes in alkali population indicates strict naturel selection. The solute carrier family 9 ( slc9) genes, especially slc9a isoform coding proteins contribute to electroneutral countertransport of H + for Na + across the plasmalemmal and organellar membranes, intracellular pH and cellular volume regulation as well as the electrolyte, acid-base, and fluid volume homeostasis at the systemic level. These functional properties determine a potential basis for organisms to challenge stressful conditions. However, these well-done researches have been reported more in mammals. Thus, in this study, a total of eleven slc9 genes were identified from the latest version genome of L. waleckii , a cyprinid fish that could tolerate extremely alkaline environments (pH 9.6). The evolutionary footprint of slc9 genes was uncovered via the analysis of copy numbers, gene structure, motif composition, chromosome location and phylogenetic relationship. More importantly, there were two SNPs located on 5’ UTR and three non-synonymous mutations in the coding region of the slc9a3.2 gene by comparing freshwater with alkaline water populations attached to resequencing technology. Slc9a3.2 gene was a statistically significant low expression in gill tissue with extremely alkaline pressure. Generally, slc9 gene family in L. waleckii was highly conserved. Several important SNPs with high Fst values were identified where non-synonymous mutations occurred between freshwater and alkaline water populations, and they may play an important role in specific functional differentiation. Slc9 genes had clear tissue expression preferences and were involved in abiotic stress response, indicating their roles in physiological function and strong self-regulating capacity. Our insight into the genetic variations that take place in the individual genes under extreme conditions could provide a feasible example for studying specific molecular mechanisms based on genomic data with increasing environmental stress.