The characteristics of mRNA m6A methylomes in allopolyploid Brassica napus and its diploid progenitors

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 m⁶A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture.

Acknowledgements

We thank Dahu Zou and Yi Li at Wuhan University and Guoliang Li at Huazhong Agricultural University for their valuable advice on data analysis. This work was supported by the National Natural Science Foundation of China (31970241).

Author contributions

This study was designed by J.W. and Z.L. Z.L. analyzed the data and wrote the manuscript. X.W. provided the experimental materials. M.L. was responsible for planting materials. M.L. provided data on histone modifications and DNA methylation. The manuscript was revised by J.W. and X.W. All authors reviewed and approved the manuscript.

Data availability

MeRIP-seq and RNA-seq data in this research have been stored in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with the accession numbers SRR16842417–SRR16842428 and SRR16842657–SRR16842668. The data on four epigenetic markers can be obtained from NCBI with the accession codes SRR13306925–SRR13306936 (WGBS) and SRR13318007–SRR13318030 (ChIP-seq).

Conflict of interest

The authors declare that they have no conflict of interest.

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