Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

Abstract

Background Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. Results In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. Conclusions Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.

Small DNA Methylation, Big Player in Plant Abiotic Stress Responses and Memory

“…Among the differentially methylated salinity-responsive genes, TaFLS1, a flavonol synthase gene, and TaWRSI5, a Bowman-Birk-type protease inhibitor, can enhance the salinity tolerance of Arabidopsis thaliana (Wang et al, 2014). In soybean root, bisulfite sequencing reveals that 61.2% of CGs, 39.7% of CHG, and 3.2% of CHHs are methylated under durable salt stress, which was slightly lower than those under control condition (Chen et al, 2019). In Rapeseed (Brassica napus var.…”

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

“…With the aid of “omics” approaches, the role of lncRNAs has been investigated in various plant species. For instance, 3030 lincRNAs and 275 lncNATs were identified from salt-stressed roots of soybean plants [ 117 ]. Salt stress also altered the accumulation of lncRNAs in Arabidopsis [ 118 ] and Medicago [ 119 ].…”

Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

“…Increasing evidence demonstrates that plant DNA methylation and demethylation are closely associated with various environmental stresses, including cold [ 7 ], drought [ 8 ], heat [ 9 ], heavy metal [ 10 ], salt [ 11 ], and ultraviolet stresses [ 12 ]. Additionally, DNA methylation and demethylation also play an indispensable role in regulating fruit development and ripening [ 3 , 13 , 14 ], as well as secondary metabolism [ 15 – 17 ].…”