Involvement of genomic variations and m6A modification in differential gene expression related to environmental responses: A subspecies-level study in plants

• Differential expression of stress-related genes was analyzed at subspecies level. • Arabidopsis and rice subspecies with distinct habitat parameters were analyzed. • The genes with higher exon numbers were more susceptible to hypo-methylation. • SNPs and m 6 A were observed to have an impact on stress-responsive gene expression. • The stress-responsive genes link to differential environmental responses in plants. Plants are sessile organisms vulnerable to environmental fluctuations. For survival, they have developed fascinating strategies to respond to the environmental stimuli. However, the molecular basis underlying the differentiated environmental responses among distinct plant species or subspecies remains under investigation. In this study, seven Arabidopsis ecotypes (Col-0 as the reference) and six rice varieties (Nipponbare as the reference) with distinct habitat parameters were selected to explore the molecular clues. Based on the transcriptome-wide m 6 A profiles, 1,428 to 3,099, and 1,295 to 2,766 differential m 6 A peaks associated with the protein-coding genes were identified from distinct subspecies of Arabidopsis and rice respectively. These peaks are highly enriched at the 3′ ends of the transcripts, and the genes containing higher numbers of the exons are more susceptible to hypo-methylation. Orthologous gene analysis showed that around 30% of the differential peak-associated genes shared common functions between Arabidopsis and rice. Functional annotations and analysis of the stress-treated methylome data supported the involvement of the differential peak-associated genes in environmental responses. In-depth mechanism study showed that both m 6 A modification and SNPs were likely to have a direct impact on differential exon expression. The influence of m 6 A modification was also observed on the expression of circRNAs whose host genes are environment-responsive. Summarily, our results provided the genomic and epitranscriptomic clues for the differential expression of the stress-responsive genes which might lead to the differential environmental responses at the subspecies level.