Li Xuexue, Liu Yuan, Liu Xuan, Sheng Huachun, Li Juan, Li Wenbing, Li Ying, Chen Chen, Feng Jingqiu, Yan Xinjia, Yang Zhengming, Huang Yanfei, Zhang Zhifeng, Zhang Shaoshan
Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Chengdu, 610225, China; Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225, China; Sichuan Ziyang Inspection and Testing Center for Food and Drug Control, Ziyang, 641399, China.
Tibetan Plateau Ethnic Medicinal Resources Protection and Utilization Key Laboratory of National Ethnic Affairs Commission of the People's Republic of China, Chengdu, 610225, China; Sichuan Provincial Qiang-Yi Medicinal Resources Protection and Utilization Technology and Engineering Laboratory, Chengdu, 610225, China.
Phytochemistry. 2025 Jul 1;239:114607. doi: 10.1016/j.phytochem.2025.114607.
Nardostachys jatamansi (D. Don) DC., an aromatic and medicinal herb belonging to the Nardostachys genus within the Caprifoliaceae family, is globally well-known for its attractive perfume and health-promoting properties. However, genomic information specific to N. jatamansi remains largely unexplored. In this study, the first de novo assembly of the N. jatamansi genome was presented which spans approximately 2.88 Gb with the contig N50 of 9.92 Mb and scaffold N50 of 40.09 Mb. Using Hi-C sequencing data, we successfully anchored 98.53 % of the assembled sequences into 78 pseudochromosomes (6n = 13), a result corroborated by chromosome (cytogenetic) analysis. The genome comprises 92.33 % repeat sequences, including 73.82 % TEs and 18.51 % tandem repeats, as well as a total of 174,054 protein-coding genes, of which 93.62 % have been functionally annotated in databases such as NR, GO, KEGG, Interpro, and others. In addition, our analysis identified 4144 tRNAs, 7537 rRNAs, 707 miRNAs, and 3400 snRNAs within the genome. Comparative genomics revealed that N. jatamansi exhibited high genetic redundancy. Phylogenetic analysis supports the current knowledge that the new APG IV classification system places N. jatamansi within the Caprifoliaceae family. Genes from the most expanded gene families, especially the TPS gene cluster at the end of chromosome 3A, are likely involved in the biosynthesis of sesquiterpenoids in N. jatamansi. Hopefully, our work would provide a valuable basis for revealing natural product-related biosynthetic pathways in N. jatamansi and advancing evolutionary studies within the Caprifoliaceae family.
甘松（Nardostachys jatamansi (D. Don) DC.）是忍冬科甘松属的一种芳香药用草本植物，以其迷人的香气和促进健康的特性而闻名于世。然而，甘松的特定基因组信息在很大程度上仍未得到探索。在本研究中，首次展示了甘松基因组的从头组装，其大小约为2.88 Gb，重叠群N50为9.92 Mb，支架N50为40.09 Mb。利用Hi-C测序数据，我们成功地将98.53%的组装序列锚定到78条假染色体（6n = 13）上，这一结果得到了染色体（细胞遗传学）分析的证实。该基因组包含92.33%的重复序列，其中包括73.82%的转座元件和18.51%的串联重复序列，以及总共174,054个蛋白质编码基因，其中93.62%已在NR、GO、KEGG、Interpro等数据库中进行了功能注释。此外，我们的分析在基因组中鉴定出4144个tRNA、7537个rRNA、707个miRNA和3400个snRNA。比较基因组学表明，甘松表现出高度的遗传冗余。系统发育分析支持了当前的认知，即新的APG IV分类系统将甘松归入忍冬科。来自扩增最多的基因家族的基因，特别是3A染色体末端的TPS基因簇，可能参与了甘松中倍半萜类化合物的生物合成。希望我们的工作能够为揭示甘松中与天然产物相关的生物合成途径以及推进忍冬科的进化研究提供有价值的基础。
