4.1 Genome-wide m6A distributions in rice
The distribution map of m6A modifications throughout the mammalian genome has been extensively assessed (Gokhale et al., 2016). Among plants, there are more reports on m6A modification sites in Arabidopsis genomic mRNA (Parker et al., 2021), and the number of reports on rice is gradually increasing (Wang et al., 2023a). We identified about 80,000 m6A modification sites in un-infested and BPH-infested Nip rice using the nanopore DRS, a powerful approach that can detect single methylation modification sites on mRNA (Supporting Information: Figure S4). Which was similar to 81,722 m6A sites previously reported in the Nipponbare rice cultivar (Yu et al., 2023). Most gene density was consistent with the density of the m6A methylome, and m6A modifications were primarily distributed on rice chromosomes 1, 2, and 3 (Figure 1e). A marked distribution pattern of m6A modifications was observed on chromosomes 1, 2, 3, 5, 6, 7, 8, and 12, which appeared as a dense and sparse distribution with higher density at both ends and lower density in the middle. Conversely, on chromosomes 4, 10, and 11, the m6A modification exhibited a distribution with a higher density on one side and a lower density on the other. These distributions may be related to the organization and arrangement of genes on the chromosomes (Figure 1e). m6A modification predominantly occurs on exons and splicing sites of RNA precursors, suggesting a certain level of selectivity in m6A modification (He et al., 2023). However, genes on different chromosomes exhibit variations in the lengths and quantities of exons and introns. Our results showed that m6A modification was most densely distributed in the CDS region, followed by that in the 3′-UTR, and least in the 5′-UTR (Supporting Information: Figure S3). This distribution pattern is conserved in several important crops, including rice (Zhang et al., 2021a), maize (Zea mays ) (Miao et al., 2020), wheat (T. aestivum ) (Zhang et al., 2021b), and tomato (Solanum lycopersicum ) (Hu et al., 2022). In mature strawberry fruit (Zhou et al., 2021), as well as in apple (Guo et al., 2022) and cabbage leaves (Liu et al., 2020a). Thus, m6A modification mainly in the CDS region may be developmental or tissue specific. The factors underlying this distribution pattern and the detailed biological functions of m6A modifications in plants remain largely unknown; these aspects require further investigation.