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.