IHB OpenIR  > 鱼类生物学及渔业生物技术研究中心  > 期刊论文
The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
Xu, Peng1,2,3,4; Xu, Jian1; Liu, Guangjian5; Chen, Lin2; Zhou, Zhixiong2; Peng, Wenzhu2; Jiang, Yanliang1; Zhao, Zixia1; Jia, Zhiying6; Sun, Yonghua7; Wu, Yidi2; Chen, Baohua2; Pu, Fei2; Feng, Jianxin8; Luo, Jing9; Chai, Jing9; Zhang, Hanyuan1; Wang, Hui2,10; Dong, Chuanju10; Jiang, Wenkai5; Sun, Xiaowen6
2019-10-11
Source PublicationNATURE COMMUNICATIONS
ISSN2041-1723
Volume10Issue:1Pages:11
Abstract

Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

DOI10.1038/s41467-019-12644-1
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; 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National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; 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National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; 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National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; 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Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; 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Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31422057] ; National Natural Science Foundation of China[31872561] ; National Natural Science Foundation of China[31502151] ; National High-Technology Research and Development Program of China[2011AA100401] ; Fundamental Research Funds for the Central Universities, Xiamen University[20720180123] ; Fundamental Research Funds for the Central Universities, Xiamen University[20720160110] ; Central Public-interest Scientific Institution Basal Research Fund, CAFS[2016HY-JC0301] ; Central Public-interest Scientific Institution Basal Research Fund, CAFS[2017B003] ; National Key Research and Development Program[2018YFD0900102]
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000489705200006
WOS KeywordGENE-EXPRESSION ; DIVERGENCE ; DUPLICATION ; DNA ; IDENTIFICATION ; SELECTION ; REVEALS ; FINDER ; TOOL ; 2R
PublisherNATURE PUBLISHING GROUP
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; 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National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; 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National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; 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National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; 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Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; National High-Technology Research and Development Program of China ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Fundamental Research Funds for the Central Universities, Xiamen University ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; Central Public-interest Scientific Institution Basal Research Fund, CAFS ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program ; National Key Research and Development Program
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/34443
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorXu, Peng
Affiliation1.Chinese Acad Fishery Sci, Key Lab Aquat Genom, Minist Agr, Beijing 100141, Peoples R China
2.Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen 361102, Fujian, Peoples R China
3.Pilot Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266071, Shandong, Peoples R China
4.Ningde Fufa Fisheries Co Ltd, State Key Lab Large Yellow Croaker Breeding, Ningde 352130, Peoples R China
5.Novogene Bioinformat Inst, Beijing 100029, Peoples R China
6.Chinese Acad Fishery Sci, Heilongjiang River Fishery Res Inst, Harbin 150001, Heilongjiang, Peoples R China
7.Chinese Acad Sci, Inst Hydrobiol, Key Lab Biodivers & Conservat Aquat Organisms, Wuhan 430072, Hubei, Peoples R China
8.Henan Acad Fishery Sci, Zhengzhou 450044, Henan, Peoples R China
9.Yunnan Univ, Ctr Life Sci, Sch Life Sci, State Key Lab Conservat & Utilizat Bioresources Y, Kunming 650091, Yunnan, Peoples R China
10.Henan Normal Univ, Coll Fisheries, Xinxiang 453007, Henan, Peoples R China
Recommended Citation
GB/T 7714
Xu, Peng,Xu, Jian,Liu, Guangjian,et al. The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio[J]. NATURE COMMUNICATIONS,2019,10(1):11.
APA Xu, Peng.,Xu, Jian.,Liu, Guangjian.,Chen, Lin.,Zhou, Zhixiong.,...&Sun, Xiaowen.(2019).The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio.NATURE COMMUNICATIONS,10(1),11.
MLA Xu, Peng,et al."The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio".NATURE COMMUNICATIONS 10.1(2019):11.
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