Salt Stress Adaptations in Soybean Involve Alterations in Pre-mRNA Processing

Salt stress can seriously affect plant survival. To adapt to salt stress, plants can alter gene expressions and/or pre-mRNA processing patterns, or both. Previous studies could not comprehensively profile stress-responsive pre-mRNA processing patterns due to limitations in traditional sequencing technologies. Now Oxford Nanopore Technologies Direct RNA Sequencing (ONT DRS) can directly sequence full-length native RNAs without requiring reverse transcription or amplification. Thus, it provides accurate profiles of pre-mRNA processing patterns at the single-molecule level. With this technology, we found more than 89 586 novel transcript isoforms in addition to the 44 877 annotated ones in soybean leaves and roots subjected to short-term salt stress. Specifically, we identified 102 191 alternative mRNA processing events and 1216 fusion transcripts corresponding to 549 genomic regions. Interestingly, genes upregulated in roots due to salt stress had longer poly(A) tail lengths and lower m6A modification ratios than controls, and downregulated genes in roots had shorter poly(A) tails. Also, the m6A modification levels changed with prolonged salt stress. Furthermore, the alteration patterns of m6A modifications under salt stress were correlated with the expressions of two m6A erasers. Our results indicated that the reshaped mRNA traits caused by salt stress could play a role in soybean adaptations.