Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness, including essential nutrients, antioxidants, and healthy fats, which boost human cardial, brain and gut health. Despite its importance, the lack of a complete genome assembly has been a stumbling block in its biological breeding process. Therefore, we generated deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads to construct a telomere-to-telomere (T2T) genome assembly. The final assembly spans 537.27 Mb with no gaps, demonstrating a remarkable completeness of 98.1 %. We utilized a combination of transcriptome data and homologous proteins to annotate the genome, identifying 36 018 protein-coding genes. Furthermore, we profiled global cytosine DNA methylations using ONT sequencing data. Global methylome analysis revealed high methylation levels in transposable element (TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas. By integrating a detailed multi-omics data analysis, we obtained valuable insights into the mechanism underlying endopleura coloration. This investigation led to the identification of eight candidate genes (e.g. ANR) involved in anthocyanin biosynthesis pathways, which are crucial for the development of color in plants. The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.

中文翻译：

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胡桃楸 （Juglans sigillata） 的端粒到端粒无间隙基因组组装


胡桃楸是一种具有经济价值的坚果作物，以其丰富的营养价值而闻名，包括必需营养素、抗氧化剂和健康脂肪，可促进人体的体质、大脑和肠道健康。尽管它很重要，但缺乏完整的基因组组装一直是其生物育种过程中的绊脚石。因此，我们生成了深度覆盖的超长牛津纳米孔技术 （ONT） 和 PacBio HiFi 读数，以构建端粒到端粒 （T2T） 基因组组装。最终组装的体积为 537.27 Mb，无间隙，完整性高达 98.1%。我们利用转录组数据和同源蛋白的组合来注释基因组，鉴定了 36 018 个蛋白质编码基因。此外，我们使用 ONT 测序数据分析了整体胞嘧啶 DNA 甲基化。整体甲基化组分析显示，富含转座因子 （TE） 的染色体区域的高甲基化水平与基因丰富区域中相对较低的甲基化并列。通过整合详细的多组学数据分析，我们获得了对内胸膜着色机制的宝贵见解。这项研究导致鉴定了八个参与花青素生物合成途径的候选基因 （例如 ANR），这些基因对植物颜色的发育至关重要。全面的基因组组装和对内胸膜着色等重要性状的遗传基础的理解将为更有效的育种计划和提高作物质量开辟途径。