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The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes has occurred in allopolyploids. What evolutionary changes have taken place in transcripts of Brassica napus during its early establishment and subsequ...

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Autores principales: Li, Mengdi, Hu, Meimei, Xiao, Yafang, Wu, Xiaoming, Wang, Jianbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923814/
https://www.ncbi.nlm.nih.gov/pubmed/35043208
http://dx.doi.org/10.1093/hr/uhab075
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author Li, Mengdi
Hu, Meimei
Xiao, Yafang
Wu, Xiaoming
Wang, Jianbo
author_facet Li, Mengdi
Hu, Meimei
Xiao, Yafang
Wu, Xiaoming
Wang, Jianbo
author_sort Li, Mengdi
collection PubMed
description Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes has occurred in allopolyploids. What evolutionary changes have taken place in transcripts of Brassica napus during its early establishment and subsequent evolution is a fascinating scientific question. Here, we study this issue using a set of materials (natural and resynthesized B. napus and their progenitors/parents) and long-read RNA sequencing technology. The results showed that more genes were upregulated in resynthesized B. napus compared with its two parents, and more upregulated expressed genes were observed in natural B. napus than in resynthesized B. napus. The presence of upregulated genes in an organism may help it to adapt to the influence of “genomic shock” and cope with the natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of the isoforms identified in all materials were novel, potentially improving the reference genome information for B. napus. We found that the isoform numbers and the numbers of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, and they may have been involved in the adaptation of plants to the natural environment. In addition, all identified isoforms were functionally annotated by searching seven databases. In general, this study can improve our overall understanding of the full-length transcriptome of B. napus and help us to recognize the significant changes in gene expression and isoform abundance that have occurred in allopolyploid B. napus during evolution.
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spelling pubmed-89238142022-03-16 The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus Li, Mengdi Hu, Meimei Xiao, Yafang Wu, Xiaoming Wang, Jianbo Hortic Res Article Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes has occurred in allopolyploids. What evolutionary changes have taken place in transcripts of Brassica napus during its early establishment and subsequent evolution is a fascinating scientific question. Here, we study this issue using a set of materials (natural and resynthesized B. napus and their progenitors/parents) and long-read RNA sequencing technology. The results showed that more genes were upregulated in resynthesized B. napus compared with its two parents, and more upregulated expressed genes were observed in natural B. napus than in resynthesized B. napus. The presence of upregulated genes in an organism may help it to adapt to the influence of “genomic shock” and cope with the natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of the isoforms identified in all materials were novel, potentially improving the reference genome information for B. napus. We found that the isoform numbers and the numbers of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, and they may have been involved in the adaptation of plants to the natural environment. In addition, all identified isoforms were functionally annotated by searching seven databases. In general, this study can improve our overall understanding of the full-length transcriptome of B. napus and help us to recognize the significant changes in gene expression and isoform abundance that have occurred in allopolyploid B. napus during evolution. Oxford University Press 2022-01-19 /pmc/articles/PMC8923814/ /pubmed/35043208 http://dx.doi.org/10.1093/hr/uhab075 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nanjing Agricultural University https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Li, Mengdi
Hu, Meimei
Xiao, Yafang
Wu, Xiaoming
Wang, Jianbo
The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title_full The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title_fullStr The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title_full_unstemmed The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title_short The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
title_sort activation of gene expression and alternative splicing in the formation and evolution of allopolyploid brassica napus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923814/
https://www.ncbi.nlm.nih.gov/pubmed/35043208
http://dx.doi.org/10.1093/hr/uhab075
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