基于全基因组InDel分析我国细鳞鲑遗传分化及本地适应性  

GENETIC DIFFERENTIATION AND LOCAL ADAPTATION OF CHINESE LENOK(BRACHYMYSTAX)POPULATIONS BASED ON WHOLE GENOME INDELS

作　　者：张鑫淼 赵春龙 谢鹏 冯广朋[4] 陈朋[5] 王立新[1] 熊冬梅 ZHANG Xin-Miao;ZHAO Chun-Long;XIE Peng;FENG Guang-Peng;CHEN Peng;WANG Li-Xin;XIONG Dong-Mei(Department of Fisheries Science,College of Animal Science and Technology,Northwest A&F University,Yangling 712100,China;Hebei Ocean and Fisheries Science Research Institute,Qinhuangdao 066200,China;College of Fisheries,Huazhong Agricultural University,Wuhan 430070,China;East China Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences,Shanghai 200090,China;Xinjiang Fisheries Research Institute,Urumqi 830000,China)

机构地区：[1]西北农林科技大学动物科技学院水产科学系,杨凌712100 [2]河北省海洋与水产科学研究院,秦皇岛066200 [3]华中农业大学水产学院,武汉430070 [4]中国水产科学研究院东海水产研究所,上海200090 [5]新疆维吾尔自治区水产科学研究所,乌鲁木齐830000

出　　处：《水生生物学报》2024年第10期1724-1735,共12页Acta Hydrobiologica Sinica

基　　金：国家自然科学基金(32273138);中央高校基本科研业务费(2452020154)资助。

摘　　要：为了从全基因组InDel角度进行全国地理尺度细鳞鲑属遗传分化与适应性研究,文章对采自陕西、甘肃、新疆、河北和黑龙江的6个细鳞鲑群体(共90尾样本)进行建库测序及InDel检测分析。结果表明:6个细鳞鲑群体共检测到3056034个高质量InDel突变位点,缺失位点数大于插入位点数,将各基因区域标准化后观察到内含子区富集到相对更多的InDel位点。所有系统发育树分支中共统计到1715464个固定的InDel,占总数的56.08%,且主要位于每个谱系的基部。群体结构分析结果显示每个细鳞鲑地理群体均具有相对独立的遗传结构。适应性分析方面:利用群体分支统计方法检测到秦岭地区细鳞鲑适应性相关的621个候选受选择基因,并筛选到两个影响外显子序列的缺失位点,分别导致insr和dnhd1缺失了两个和一个氨基酸密码子。对所有候选受选择基因的富集分析结果显示主要在神经发育和代谢等途径发挥作用。研究可为秦岭细鳞鲑山区溪流生境适应性候选基因的深入挖掘及人工增殖和保护中分子标记的开发提供基础资料,也为进一步厘清细鳞鲑属物种分化提供参考。To study the genetics and evolution of the genus Brachymystax at the national geographic scale from the perspective of InDel in genome-wide,we employed whole genome resequencing and InDel detection analysis on six Brachymystax populations(a total of 90 samples)collected from Shaanxi,Gansu,Xinjiang,Hebei and Heilongjiang.The aim was to provide new insights into the genetic differentiation and local adaptation of Brachymystax populations through the perspective of InDels.Results showed the detection of a total of 3056034 high-quality InDel mutation sites among the six Brachymystax populations,with deletions exceeding insertions.After standardizing various gene regions,it was observed that intronic regions exhibited a relatively higher concentration of InDel sites.A total of 1715464 fixed InDels were identified in all branches of the phylogenetic tree,accounting for 56.08%of the total,primarily situated at the base of each lineage.Population structure analysis revealed that each geographic population of Brachymystax displayed a relatively distinct genetic structure.Regarding adaptive analysis,621 candidate selection genes associated with local adaptation were detected using population branch statistics.Notably,two deletions affecting exonic sequences were identified,resulting in the loss of two and one amino acid codons in insr and dnhd1,respectively.Enrichment analysis of all potentially selective genes highlighted their significant involvement in pathways such as neural development and metabolism.This study provides foundational information for the comprehensive exploration of candidate adaptive genes in the mountain stream habitats of Qinling lenok,alongside facilitating the development of molecular markers for artificial breeding and conservation efforts.Additionally,it serves as a reference for further clarification of species differentiation within the genus Brachymystax.

关 键 词：INDEL 全基因组重测序 种群结构 本地适应 细鳞鲑 

分 类 号：Q346.5[生物学—遗传学]