The Allotetraploid Origin and Asymmetrical Genome Evolution of The common Carp Cyprinus Carpio

Overview

Journal Nat Commun

Specialty Biology

Date 2019 Oct 13

PMID 31604932

Citations 85

Authors

Peng Xu

Jian Xu

Guangjian Liu

Lin Chen

Zhixiong Zhou

Wenzhu Peng

Yanliang Jiang

Zixia Zhao

Zhiying Jia

Yonghua Sun

Yidi Wu

Baohua Chen

Fei Pu

Jianxin Feng

Jing Luo

Jing Chai

Hanyuan Zhang

Hui Wang

Chuanju Dong

Wenkai Jiang

Xiaowen Sun

Affiliations

Soon will be listed here.

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.

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