Chromosome-level genome of Nardostachys jatamansi and comparative genomics analysis reveals its sesquiterpenoid...

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.