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Article|11 Oct 2022|OPEN
The characteristics of mRNA m6A methylomes in allopolyploid Brassica napus and its diploid progenitors
Zeyu Li1 , Mengdi Li1,2 and Xiaoming Wu3 , Jianbo Wang,1 ,
1State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
2Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
3Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
*Corresponding author. E-mail: jbwang@whu.edu.cn

Horticulture Research 10,
Article number: uhac230 (2023)
doi: https://doi.org/10.1093/hr/uhac230
Views: 311

Received: 18 May 2022
Accepted: 30 Sep 2022
Published online: 11 Oct 2022

Abstract

Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m6A modification, the most widespread internal eukaryotic mRNA modification, in polyploid species are still poorly understood. This study revealed the characteristics of m6A methylomes within the early formation and following the evolution of allopolyploid Brassica napus. We found a complex relationship between m6A modification abundance and gene expression level depending on the degree of enrichment or presence/absence of m6A modification. Overall, the m6A genes had lower gene expression levels than the non-m6A genes. Allopolyploidization may change the expression divergence of duplicated gene pairs with identical m6A patterns and diverged m6A patterns. Compared with duplicated genes, singletons with a higher evolutionary rate exhibited higher m6A modification. Five kinds of duplicated genes exhibited distinct distributions of m6A modifications in transcripts and gene expression level. In particular, tandem duplication-derived genes showed unique m6A modification enrichment around the transcript start site. Active histone modifications (H3K27ac and H3K4me3) but not DNA methylation were enriched around genes of m6A peaks. These findings provide a new understanding of the features of m 6A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture.