N⁶-methyladenine (6mA) is one of the epigenetic modifications. Although 6mA was discovered at the same time as 5-methylcytosine (5mC), it has only received recent attention in eukaryotes mainly due to the limitation of detection technology. The methylation of genomic DNA plays a crucial role in gene regulation and genome stability for eukaryotes. Nevertheless, how 6mA methylation on genes across the genome evolves during species divergence and different duplicate gene divergence is unclear.

To understand the evolution of 6mA methylation, research teams from Wuhan Botanical Garden and the Chinese Academy of Agricultural Sciences studied the differences in 6mA methylation within four Nelumbo nucifera wild species and patterns of 6mA methylation between N. nucifera, Arabidopsis thaliana, and Oryza sativa orthologs.

In this study, four high-quality lotus reference genomes were sequenced and assembled into pseudochromosome using Oxford Nanopore Technologies long-read sequencing.

Distribution analysis detects no similarity between 6mA sites and the widely studied 5mC methylation sites in lotus. Consistently, 6mA sites are enriched at the start sites, positively correlated to gene expression and preferentially retained in highly and broadly expressed genes with long lengths among distantly related plants. Among different duplicate genes, 6mA modifications are more likely to be retained in whole-genome duplications than locally duplicated genes and during the long-term evolution of plant species.

The research was funded by the Strategic Priority Research Program of Chinese Academy of Sciences, the National Natural Science Foundation of China, and the Youth Innovation Promotion Association of Chinese Academy of Sciences.

The results have been published in Plants entitled “6mA DNA methylation on genes in plants is associated with gene complexity, expression and duplication”.