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Whole-genome bisulfite sequencing reveals dynamic DNA methylation changes in Vigna radiata under direct and pre-conditioned salt stress

ABSTRACT: DNA methylation is an important epigenetic mechanism regulating gene expression and stress memory in plants. To investigate the role of DNA methylation in salt stress adaptation, we performed whole-genome bisulfite sequencing (WGBS) of mung bean (Vigna radiata cv. Weilv 9) leaves under two treatment regimes: T1 (pre-conditioned with 100 mM NaCl for 24 h, recovered for 48 h, then re-exposed to 100 mM NaCl) and T2 (direct exposure to 100 mM NaCl without preconditioning). Seedlings were grown hydroponically in half-strength Murashige and Skoog medium under controlled environmental conditions. Genomic DNA was extracted from the first fully expanded true leaves at 0, 6, and 48 h after the onset of the final salt treatment, with three biological replicates per condition. Bisulfite-converted DNA was sequenced to generate genome-wide methylation profiles. Comparative analysis revealed dynamic changes in CG, CHG, and CHH contexts, providing insights into the epigenetic basis of salt tolerance and stress priming in legumes.

ORGANISM(S): Vigna radiata

PROVIDER: GSE334479 | GEO | 2026/06/07

REPOSITORIES: GEO

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Project description:RNA Seq was extracted from cucumber leaves after 7 days of bacteria inoculated in shoot and salt stress treatment. There were four treatment in this study, : ‘CK’ stands for seedlings under 0 mM NaCl without BC56 inoculation; ‘BC56’ refers to seedlings under 0 mM NaCl with BC56 inoculation; ‘Salt’ means seedlings under 100 mM NaCl without BC56 inoculation; ‘BC56+Salt’ indicates seedlings under 100 mM NaCl with BC56 inoculation.GO was used to assign putative functions to all identified DEGs into three principal categories, namely cellular component, molecular function, and biological process. An analysis of the GO terms suggested that ‘nucleus’, ‘plasma membrane’, and ‘integral component of membrane’ were the most dominant terms in the cellular component. While ‘biological process’, ‘regulation of transcription, DNA -templated’ and ‘transcription, DNA-templated’ were the most abundant terms in the biological process. In addition ‘molecular function’, ‘protein binding’ and ‘DNA-binding transcription factor activity’ were the major terms in the molecular function category. KEGG pathway analysis of DEGs in different comparison group suggested that in the BC56 vs CK comparison group DEGs were mainly enriched in four pathways which are ‘photosynthesis - antenna proteins’, ‘phenylpropanoid biosynthesis’, ‘metabolic pathways’ and ‘MAPK signaling pathway – plant’. In the BC56 vs CK comparison group DEGs were mainly enriched in seven pathways which are ‘phenylpropanoid biosynthesis’, ‘plant hormone signal transduction’, ‘biosynthesis of secondary metabolites’, ‘flavonoid biosynthesis’, ‘metabolic pathways’, ‘carotenoid biosynthesis’ and ‘stilbenoid, diarylheptanoid and gingerol biosynthesis’. In addition, compared with BC56+Salt vs CK, ‘ABC transporters’, ‘nitrogen metabolism’ and ‘phenylalanine metabolism’ is only significantly enriched in Salt vs CK.

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Whole-genome bisulfite sequencing reveals dynamic DNA methylation changes in Vigna radiata under direct and pre-conditioned salt stress

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