National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
Plant Genome. 2022 Sep;15(3):e20207. doi: 10.1002/tpg2.20207. Epub 2022 Jul 5.
Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features- slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly-methylated genes showed lowest expression. Transposable element (TE)-related genes were methylated in multiple contexts and hence classified as C-methylated genes. A low expression among C-methylated genes was associated with transposons insertion in gene-body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non-CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen-related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
兵豆（Cajanus cajan L. Huth）是一种在全世界广泛种植的重要豆科作物。在这项研究中，我们对兵豆的基因体甲基化（GbM）模式进行了广泛分析。我们发现 CG 和 CHG 甲基化模式呈双峰分布。GbM 特征——缓慢的进化速度和增加的长度保持保守。具有中度 CG 体甲基化的基因表现出最高的表达水平，而高度甲基化的基因表现出最低的表达水平。转座元件（TE）相关基因在多个背景下被甲基化，因此被归类为 C 甲基化基因。C 甲基化基因的低表达与基因体和上游调控区中转座子的插入有关。与非 CG 甲基化相比，CG 甲基化模式在同源物中是保守的。通过比较三种基因型差异甲基化区域（DMR）之间的甲基化模式，我们发现可变甲基化标记不太可能靶向进化保守序列。最后，我们的分析表明，氮相关基因在豆科植物的 GbM 同源物中富集，这些基因可能是产生作物改良的表观等位基因的有前途的候选基因。
