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

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

doi:10.24272/j.issn.2095-8137.2022.462

Volume 44 Issue 2

Mar. 2023

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Article Navigation > Zoological Research > 2023 > 44(2): 287-302

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. Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species. Zoological Research, 2023, 44(2): 287-302. doi: 10.24272/j.issn.2095-8137.2022.462

Citation:

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. Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species. Zoological Research, 2023, 44(2): 287-302. doi: 10.24272/j.issn.2095-8137.2022.462

Citation:

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. Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species. Zoological Research, 2023, 44(2): 287-302. doi: 10.24272/j.issn.2095-8137.2022.462

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

doi: 10.24272/j.issn.2095-8137.2022.462

Guang-Xian Tu^{1, 2},
Xin-Shuang Zhang³,
Rui-Run Jiang^{1, 2},
Long Zhang^{1, 2},
Cheng-Jun Lai^{1, 2},
Zhu-Yue Yan^{1, 2},
Yan-Rong Lv^{1, 2},
Shao-Ping Weng^{1, 2, 4},
Li Zhang³,
Jian-Guo He^{1, 2, 4
,
,},
Muhua Wang^{1, 2, 4
,
,}

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

Raw reads and genome assemblies are accessible at the NCBI database under BioProjectID PRJNA867131. Raw reads and genome assemblies are also available at the Genome Sequence Archive (GSA) database of the National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession number PRJCA013257 and the Science Data Bank (https://www.scidb.cn/en) under DOI: 10.57760/sciencedb.06965. The genome assembly, related annotation files, and source files for generating figures can be accessed through Figshare at https://doi.org/10.6084/m9.figshare.21385059.
Supplementary data to this article can be found online.

Funds: This study was 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), and Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (311021006)

More Information

Corresponding author: E-mail: lsshjg@mail.sysu.edu.cn; wangmuh@mail.sysu.edu.cn
Received Date: 2022-12-16
Accepted Date: 2023-02-13

Published Online: 2023-02-11

Publish Date: 2023-03-18

Abstract

Abstract

Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on cis-regulatory divergence 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 and 740.54 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.
- cis-regulatory divergence,
- Structural variants,
- H3K27ac,
- Broad H3K4me3,
- Siniperca chuatsi,
- Siniperca scherzeri

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References(135)

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