Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

作     者：Guang-Xian Tu Xin-Shuang Zhang Rui-Run Jiang Long Zhang Cheng-Jun Lai Zhu-Yue Yan Yan-Rong Lv Shao-Ping Weng Li Zhang Jian-Guo He Muhua Wang Guang-Xian Tu;Xin-Shuang Zhang;Rui-Run Jiang;Long Zhang;Cheng-Jun Lai;Zhu-Yue Yan;Yan-Rong Lv;Shao-Ping Weng;Li Zhang;Jian-Guo He;Muhua Wang

作者机构：State Key Laboratory for BiocontrolSchool of Marine SciencesSun Yat-sen UniversityZhuhaiGuangdong 519000China China-ASEAN Belt and Road Joint Laboratory on Mariculture TechnologySouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai)ZhuhaiGuangdong 519000China Chinese Institute for Brain ResearchBeijing 102206China Guangdong Province Key Laboratory for Aquatic Economic AnimalsSchool of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2023年第44卷第2期

页      面：287-302页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 0905[农学-畜牧学] 09[农学] 071007[理学-遗传学] 090501[农学-动物遗传育种与繁殖] 

基　　金：supported by the National Natural Science Foundation of China (31900309) Guangdong Basic and Applied Basic Research Foundation (2019A1515011644) Key-Area Research and Development Program of Guangdong Province (2021B0202020001) Seed Industry Development Project of Agricultural and Rural Department of Guangdong Province (2022) Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)(311021006) 

主　　题：cis-regulatory divergence Structural variants H3K27ac Broad H3K4me3 Siniperca chuatsi Siniperca scherzeri 

摘      要：Due to the difficulty in accurately identifying structural variants(SVs) across genomes,their impact on cisregulato ry diverge n ce of closely related species,especially fish,remains to be *** identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological ***,the role of broad H3K4me3 domains in phenotypic divergence remains poorly *** chuatsi and *** are closely related but divergent in several phenotypic traits,making them an ideal model to study cis-regulatory evolution in sister ***,we generated chromosome-level genomes of *** and ***,with assembled genome sizes of 716.35 and740.54 Mb,*** evolutionary histories of *** and *** were studied by inferring dynamic changes in ancestral population *** explore the genetic basis of adaptation in *** and ***,we performed gene family expansion and contraction analysis and identified positively selected genes(PSGs).To investigate the role of SVs in cis-regulatory divergence of closely related fish species,we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of *** and *** analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between *** and ***,divergent broad H3K4me3 domains were mostly associated with cancer-related genes in *** and *** and contributed to their phenotypic divergence.