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Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and t...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group US
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8492472/ https://www.ncbi.nlm.nih.gov/pubmed/34594040 http://dx.doi.org/10.1038/s41588-021-00933-9 |
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author | Li, Jiong-Tang Wang, Qi Huang Yang, Mei-Di Li, Qing-Song Cui, Ming-Shu Dong, Zai-Jie Wang, Hong-Wei Yu, Ju-Hua Zhao, Yu-Jie Yang, Chen-Ru Wang, Ya-Xin Sun, Xiao-Qing Zhang, Yan Zhao, Ran Jia, Zhi-Ying Wang, Xi-Yin |
author_facet | Li, Jiong-Tang Wang, Qi Huang Yang, Mei-Di Li, Qing-Song Cui, Ming-Shu Dong, Zai-Jie Wang, Hong-Wei Yu, Ju-Hua Zhao, Yu-Jie Yang, Chen-Ru Wang, Ya-Xin Sun, Xiao-Qing Zhang, Yan Zhao, Ran Jia, Zhi-Ying Wang, Xi-Yin |
author_sort | Li, Jiong-Tang |
collection | PubMed |
description | How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate. |
format | Online Article Text |
id | pubmed-8492472 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group US |
record_format | MEDLINE/PubMed |
spelling | pubmed-84924722021-10-14 Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish Li, Jiong-Tang Wang, Qi Huang Yang, Mei-Di Li, Qing-Song Cui, Ming-Shu Dong, Zai-Jie Wang, Hong-Wei Yu, Ju-Hua Zhao, Yu-Jie Yang, Chen-Ru Wang, Ya-Xin Sun, Xiao-Qing Zhang, Yan Zhao, Ran Jia, Zhi-Ying Wang, Xi-Yin Nat Genet Article How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate. Nature Publishing Group US 2021-09-30 2021 /pmc/articles/PMC8492472/ /pubmed/34594040 http://dx.doi.org/10.1038/s41588-021-00933-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Li, Jiong-Tang Wang, Qi Huang Yang, Mei-Di Li, Qing-Song Cui, Ming-Shu Dong, Zai-Jie Wang, Hong-Wei Yu, Ju-Hua Zhao, Yu-Jie Yang, Chen-Ru Wang, Ya-Xin Sun, Xiao-Qing Zhang, Yan Zhao, Ran Jia, Zhi-Ying Wang, Xi-Yin Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title | Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title_full | Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title_fullStr | Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title_full_unstemmed | Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title_short | Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
title_sort | parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8492472/ https://www.ncbi.nlm.nih.gov/pubmed/34594040 http://dx.doi.org/10.1038/s41588-021-00933-9 |
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