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