ONT direct RNA sequencing of soybean under salt stress

Gene expression and regulation is crucial for plant adaptation to adverse habitats. Besides alternative splicing, poly(A) tail length and m6A modifications also were suggested to contribute to gene expression and regulation. However, previous mRNA sequencing approach could not concurrently profile all these RNA processing events. Here, we used Oxford Nanopore Technologies Direct RNA Sequencing (ONT DRS) to profile (epi- )transcriptomes of leaves and roots of cultivar soybean under short-term (1hour) salt stress, found that salt stress could lead to not only the alternative splicing events, but also poly(A) tail length alteration and m6A modification changes of transcripts of those up- or down- regulated genes. Comparing to root mock samples, transcripts of upregulated genes in 1h salt stressed root samples have longer poly(A) tail length, while transcripts of downregulated genes in 1h salt stressed root samples have shorter poly(A) tail length comparing to those in root mock samples. Interestingly, m6A modification levels in the transcripts of upregulated genes in the 1h salt stressed root samples decreased comparing to root mock samples. The anti-correlation between poly(A) tail length and m6A modification levels for transcripts of up- or down-regulated genes indicates that soybean may regulate gene expression and mRNA stability under salt stress also via alterations of poly(A) tail length and m6A modification levels, at least for up-regulated genes in roots. Our results provide additional dimensions to investigate soybean gene expression and regulation at mRNA levels.