Grafting is an ancient technique used for plant propagation and improvement in horticultural crops for at least 1,500 years. Citrus plants, with a seed-to-seed cycle of 5–15 years, are among the fruit crops that were probably domesticated by grafting. Poncirus trifoliata, a widely used citrus rootstock, can promote early flowering, strengthen stress tolerance, and improve fruit quality via scion–rootstock interactions. Here, we report its genome assembly using PacBio sequencing. We obtained a final genome of 303 Mb with a contig N50 size of 1.17 Mb and annotated 25,680 protein-coding genes. DNA methylome and transcriptome analyses indicated that the strong adaptability of P. trifoliata is likely attributable to its special epigenetic modification and expression pattern of resistance-related genes. Heterografting by using sweet orange as scion and P. trifoliata as rootstock and autografting using sweet orange as both scion and rootstock were performed to investigate the genetic effects of the rootstock. Single-base methylome analysis indicated that P. trifoliata as a rootstock caused DNA demethylation and a reduction in 24-nt small RNAs (sRNAs) in scions compared to the level observed with autografting, implying the involvement of sRNA-mediated graft-transmissible epigenetic modifications in citrus grafting. Taken together, the assembled genome for the citrus rootstock and the analysis of graft-induced epigenetic modifications provide global insights into the genetic effects of rootstock–scion interactions and grafting biology.

中文翻译：

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柑橘砧木基因组和异种移植引起的整体 DNA 去甲基化

嫁接是一种古老的技术，用于植物繁殖和园艺作物改良至少有 1,500 年的历史。柑橘类植物的种子到种子周期为 5-15 年，属于可能通过嫁接驯化的水果作物。三叶枸杞, 是一种广泛使用的柑橘砧木，可通过接穗与砧木的相互作用促进早花、增强抗逆性和提高果实品质。在这里，我们使用 PacBio 测序报告其基因组组装。我们获得了 303 Mb 的最终基因组，contig N50 大小为 1.17 Mb，并注释了 25,680 个蛋白质编码基因。DNA甲基化组和转录组分析表明，三叶杨可能归因于其特殊的表观遗传修饰和抗性相关基因的表达模式。以甜橙为接穗进行异种嫁接，三叶杨作为砧木和使用甜橙作为接穗和砧木的自体嫁接，以研究砧木的遗传效应。单碱基甲基化组分析表明三叶杨与自体嫁接观察到的水平相比，作为砧木导致 DNA 去甲基化和接穗中 24-nt 小 RNA (sRNA) 的减少，这意味着 sRNA 介导的嫁接可传递的表观遗传修饰参与了柑橘嫁接。总之，柑橘砧木的组装基因组和嫁接诱导的表观遗传修饰分析为砧木-接穗相互作用和嫁接生物学的遗传效应提供了全球见解。