Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue. We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes. This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.

中文翻译：

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在葡萄胚胎发生愈伤组织中，转座因子的转录升高伴随着 het-siRNA 驱动的从头 DNA 甲基化

体细胞变异是克隆繁殖作物性状多样性的重要来源。在已经在世界范围内克隆繁殖数百年的葡​​萄藤中，白色浆果颜色等重要表型是由转座因子引起的遗传变化的结果。此外，外等位基因的形成可能在决定葡萄的地理特异性（“风土”）差异中发挥作用，从而最终在葡萄酒中发挥作用。这种基因组可塑性可能会通过体细胞胚胎发生用于作物改良，但这取决于对这些培养物中转座元件 (TE) 表达和沉默的表观遗传调控的物种特异性理解。为此，我们使用全基因组亚硫酸氢盐测序、mRNA 测序和小 RNA 测序来研究胚性愈伤组织中 TEs 的表观遗传状态和表达，与叶组织相比。我们发现，与叶组织相比，葡萄胚胎发生愈伤组织培养物积累了相对较高的全基因组 CHH 甲基化，尤其是跨异染色质区域。这种从头甲基化与来自高度复制的 TE 家族以及相应的 24 nt 异染色质 siRNA 的大量转录本相关。TE 特异性 CHG 环境中的甲基化相对于位于基因内的 TE 而言相对较低，并且基因内 TE 基因座的表达与这些基因的表达高度相关。这种葡萄胚胎发生愈伤组织与叶组织相比的多组学分析揭示了 TE 的高水平全基因组转录，伴随着这些序列的 RNA 依赖性 DNA 甲基化。