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 

机构地区：[1]State Key Laboratory for Biocontrol,School of Marine Sciences,Sun Yat-sen University,Zhuhai,Guangdong 519000,China [2]China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai),Zhuhai,Guangdong 519000,China [3]Chinese Institute for Brain Research,Beijing 102206,China [4]Guangdong Province Key Laboratory for Aquatic Economic Animals,School of Life Sciences,Sun Yat-sen University,Guangzhou,Guangdong 510275,China

出　　处：《Zoological Research》2023年第2期287-302,共16页动物学研究（英文）

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)。

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 explored.Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes.However,the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood.Siniperca chuatsi and S.scherzeri are closely related but divergent in several phenotypic traits,making them an ideal model to study cis-regulatory evolution in sister species.Here,we generated chromosome-level genomes of S.chuatsi and S.scherzeri,with assembled genome sizes of 716.35 and740.54 Mb,respectively.The evolutionary histories of S.chuatsi and S.scherzeri were studied by inferring dynamic changes in ancestral population sizes.To explore the genetic basis of adaptation in S.chuatsi and S.scherzeri,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 S.chuatsi and S.scherzeri.Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between S.chuatsi and S.scherzeri.Additionally,divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S.chuatsi and S.scherzeri and contributed to their phenotypic divergence.

关 键 词：cis-regulatory divergence Structural variants H3K27ac Broad H3K4me3 Siniperca chuatsi Siniperca scherzeri 

分 类 号：Q953[生物学—动物学]