The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Thus, this research was undertaken to study level and pattern of site-specific cytosine methylation of ITS1, 5.8S and ITS2 in nine tissues and/or developmental stage of pepper Capsicum annuum L. cultivar Demre Sivrisi. Tissues studied consisted of young and old roots at 30 and 90 days after sowing (das), mature dry seeds and seeds at 26 days of post anthesis (dpa), flowering buds at 1 day before flowering, pericarps at 3, 15 and 65 dpa. Levels and patterns of DNA cytosine methylation were identified at single base resolution using bisulfite conversion sequencing. Results of this study revealed that DNA cytosine level and pattern of ITS1, 5.8S and ITS2 were different in most tissues and/or developmental stages studied. In addition, methylation levels of CG, CHG and CHH contexts were also significantly different among the regions. Based on the findings of this study, it was concluded that high level of methylation of nrDNA sequences was relatively higher as observed in transposable element and promoter. On the other hand, its tissue-specific gene expression was effective as that of gene body and promoter methylation. Overall findings revealed that methylation levels of nrDNA could be used as biomarkers for tissue identification or age estimation in plants.

核糖体DNA（nrDNA）序列通常用于生物之间的系统发育分析。由于DNA胞嘧啶甲基化和核仁优势是nrDNA的两个常见表观遗传机制，我们假设nrDNA序列的内部转录间隔区1（ITS1），5.8S rRNA和ITS2可用作表观遗传标志。因此，本研究旨在研究辣椒辣椒的9个组织和/或发育阶段中ITS1、5.8S和ITS2的位点特异性胞嘧啶甲基化的水平和模式。L.栽培品种Demre Sivrisi。研究的组织包括播种后30和90天的幼根和老根（das），成熟的干种子和花后26天的种子（dpa），开花前1天的花蕾，果皮3、15和65 dpa 。使用亚硫酸氢盐转化测序，以单碱基分辨率鉴定了DNA胞嘧啶甲基化的水平和模式。这项研究的结果表明，在大多数研究的组织和/或发育阶段，ITS1、5.8S和ITS2的DNA胞嘧啶水平和模式是不同的。此外，各地区CG，CHG和CHH环境的甲基化水平也存在显着差异。根据本研究的发现，可以得出结论，如在转座因子和启动子中观察到的，nrDNA序列的甲基化水平较高。另一方面，它的组织特异性基因表达与基因体和启动子甲基化一样有效。总体发现表明，nrDNA的甲基化水平可以用作植物识别或年龄估算的生物标记。