Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping‐by‐sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context‐specific DNA methylation at the single‐base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10‐fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long‐terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome‐level structural and functional aspects of methylation in barley.

中文翻译：

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新的具有代表性的亚硫酸氢盐测序管道WellMeth揭示了春季大麦的胞嘧啶甲基化情况

在植物中，胞嘧啶甲基化的模式和水平差异很大，并且与基因组大小以及基因组中转座子和其他重复元件的比例有关。我们探索了代表性的春季大麦（大麦（Hordeum vulgare）L.）基因组跨越多个商业和历史品种。这项研究采用了基因分型测序（GBS）方法来检测基因组DNA中的甲基化胞嘧啶。为了分析数据，我们开发了WellMeth，这是一个完整的流水线，用于分析还原表示的亚硫酸氢盐测序。WellMeth能够以单碱基分辨率对上下文特定的DNA甲基化进行定量，并能够鉴定差异甲基化位点（DMC）和区域（DMR）。平均而言，DNA甲基化水平明显高于许多植物物种中常见的水平，比拟南芥中的水平高出十倍以上（L.）Heynh。在CHH甲基化中。在长末端重复（LTR）逆转录转座子吉普赛和科皮亚的边缘内和边缘观察到优先甲基化。从品种的成对比较中，可以鉴定出许多DMR，其中在分析的大麦品种集中保存了超过5,000个DMR。与基因重叠的区域子集显示出与染色质，细胞结构和组织相关的基因本体（GO）类别的丰富。遗传距离与表观遗传距离之间的显着相关性表明，大麦中相当一部分甲基化区域处于严格的遗传控制之下。本文提供的数据代表着努力更好地了解大麦甲基化的基因组水平结构和功能方面的第一步。