Differential DNA methylation and transcription profiles in date palm roots exposed to salinity

As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation. To achieve these, whole-genome bisulfite sequencing (WGBS) was employed and mRNA was sequenced from salinity-treated and untreated roots. The WGBS analysis included 324,987,795 and 317,056,091 total reads of the control and the salinity-treated samples, respectively. The analysis covered about 81% of the total genomic DNA with about 40% of mapping efficiency of the sequenced reads and an average read depth of 17-fold coverage per DNA strand, and with a bisulfite conversion rate of around 99%. The level of methylation within the differentially methylated regions (DMRs) was significantly (p < 0.05, FDR ≤ 0.05) increased in response to salinity specifically at the mCHG and mCHH sequence contexts. Consistently, the mass spectrometry and the enzyme-linked immunosorbent assay (ELISA) showed that there was a significant (p < 0.05) increase in the global DNA methylation in response to salinity. mRNA sequencing revealed the presence of 6,405 differentially regulated genes with a significant value (p < 0.001, FDR ≤ 0.05) in response to salinity. Integration of high-resolution methylome and transcriptome analyses revealed a negative correlation between mCG methylation located within the promoters and the gene expression, while a positive correlation was noticed between mCHG/mCHH methylation rations and gene expression specifically when plants grew under control conditions. Therefore, the methylome and transcriptome relationships vary based on the methylated sequence context, the methylated region within the gene, the protein-coding ability of the gene, and the salinity treatment. These results provide insights into interplay among DNA methylation and gene expression, and highlight the effect of salinity on the nature of this relationship, which may involve other genetic and epigenetic players under salt stress conditions. The results obtained from this project provide the first draft map of the differential methylome and transcriptome of date palm when exposed to an abiotic stress.

作为一种耐盐植物，海枣（Phoenix dactylifera L.）需要相应的适应性机制以应对盐渍土壤的胁迫。日益增多的研究证据表明，DNA甲基化在调控植物响应包括盐胁迫在内的非生物胁迫的基因表达过程中发挥着关键作用。因此，本研究旨在探究海枣基因组在暴露于盐胁迫时的差异甲基化状态，并鉴定受DNA甲基化调控的盐响应基因。为达成上述研究目标，本研究采用全基因组亚硫酸氢盐测序（whole-genome bisulfite sequencing, WGBS）技术，并对盐胁迫处理与未处理的海枣根系进行mRNA测序。WGBS分析结果显示，对照组与盐胁迫处理组的总测序读数分别为324,987,795和317,056,091；该分析覆盖了约81%的基因组DNA，测序读数的比对效率约为40%，每条DNA链的平均测序深度为17倍覆盖度，亚硫酸氢盐转化率约为99%。差异甲基化区域（differentially methylated regions, DMRs）内的甲基化水平在盐胁迫响应下显著升高（p < 0.05，错误发现率（False Discovery Rate, FDR） ≤ 0.05），且该升高特异性地出现在mCHG和mCHH序列背景中。与此一致的是，质谱分析与酶联免疫吸附测定（enzyme-linked immunosorbent assay, ELISA）结果证实，盐胁迫下植株的全局DNA甲基化水平显著升高（p < 0.05）。mRNA测序共鉴定出6,405个差异调控基因，其响应盐胁迫的显著性满足p < 0.001且FDR ≤ 0.05。整合高分辨率甲基化组与转录组的分析结果显示，位于启动子区域的mCG甲基化与基因表达呈负相关；而在对照条件下生长的植株中，mCHG/mCHH甲基化比率与基因表达呈正相关。甲基化组与转录组的关联模式会因甲基化序列背景、基因内甲基化区域、基因的蛋白编码能力以及盐胁迫处理的不同而有所差异。本研究结果揭示了DNA甲基化与基因表达之间的互作机制，并阐明了盐胁迫对该关联模式的调控作用，该过程在盐胁迫条件下可能还涉及其他遗传与表观遗传调控因子。本项目所得结果首次绘制了海枣在暴露于非生物胁迫时的差异甲基化组与转录组草图。