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The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

文献类型： 外文期刊

作者： Xu, Peng 1 ; Xu, Jian 1 ; Liu, Guangjian 5 ; Chen, Lin 2 ; Zhou, Zhixiong 2 ; Peng, Wenzhu 2 ; Jiang, Yanliang 1 ; Zhao, 1 ;

作者机构： 1.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

期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.919； 五年影响因子：15.805 ）

ISSN： 2041-1723

年卷期： 2019 年 10 卷

页码：

收录情况： SCI

摘要： 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.

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