The telomere-to-telomere gap-free genome assembly of Juglans sigillata

• 發表在: Horticultural Plant Journal
• Main Authors: Delu Ning, Tao Wu, Wenlong Lei, Shengcheng Zhang, Ting Ma, Li Pan, Liangjun Xiao, Noor-ul- Ain, Xingtan Zhang, Fuliang Cao
• 格式: Article
• 語言: 英语
• 出版: KeAi Communications Co., Ltd. 2025-07-01
• 主題: Juglans sigillata; Telomere-to-telomere (T2T) genome assembly; Global methylation; Endopleura color
• 在線閱讀: http://www.sciencedirect.com/science/article/pii/S246801412400219X

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.