Author:
Ren Li,Gao Xin,Cui Jialin,Zhang Chun,Dai He,Luo Mengxue,He Shaofang,Qin Qinbo,Luo Kaikun,Tao Min,Xiao Jun,Wang Jing,Zhang Hong,Zhang Xueyin,Zhou Yi,Wang Jing,Zhao Xin,Liu Guiming,Wang Guoliang,Huo Linhe,Wang Shi,Hu Fangzhou,Zhao Rurong,Zhou Rong,Wang Yude,Liu Qinfeng,Yan Xiaojing,Wu Chang,Yang Conghui,Tang Chenchen,Duan Wei,Liu Shaojun
Abstract
Abstract
Background
Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids.
Results
We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis.
Conclusions
Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.
Funder
National Natural Science Foundation of China
China Agriculture Research System
Huxiang Young Talent Project of China
Hunan Provincial Science and Technology Department of China
Key Research and Development Program of Hunan Province of China
National Key R&D Program of China
High-Level Talent Agglomeration Program of Hunan, China
Resources Sharing Service Platform of Science and Technology in Hunan Province of China
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Developmental Biology,Plant Science,General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Physiology,Ecology, Evolution, Behavior and Systematics,Structural Biology,Biotechnology
Cited by
3 articles.
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