Genome-Wide Analysis of DNA Methyltransferases in a Model Extremophyte, Schrenkiella Parvula: Transcriptional Dynamics during Development and under Salt Stress

Abstract

DNA methyltransferases (DMTs) are involved in plant stress response and development. Schrenkiella parvula, a model extremophyte, thrives under various stresses. However, the interplay between stress tolerance and epigenetic mechanisms remains elusive in extremophytes. In this study, DNA methyltransferases were identified in S. parvula for the first time and classified into 4 subfamilies: two methyltransferases (METs), three chromomethylases (CMTs), three domains rearranged methyltransferases (DRMs), and one DNA methyltransferase 2 (DNMT2). The predicted molecular weights (MWs) ranged from 43.54 (SpDNMT2) to 176.58 (SpMET2) kDa. Analysis of evolutionary selective pressure determined that the Ka/Ks values were lower than 1, indicating a strong negative selection during evolution. The cis-elements were associated with stress-response, hormonal regulation, light-response, and development. Spatiotemporal RNA-seq analysis revealed differential expression of DMTs under NaCl stress. In siliques treated with 150 mM NaCl before flowering, MET1, MET2, CMT1, and DRM2 showed downregulation in expression, while in siliques treated after flowering, DRM1 and DRM2 exhibited downregulation. The MET1 gene is specifically expressed in siliques. Gene expression patterns were dependent on tissue type, developmental stage, and the duration of salt stress. Differences in transcript levels of SpDMT genes under NaCl stress, along with cis-elements, suggest that SpDMTs might be involved in salt stress adaptation.