Telomere-to-Telomere Genome Assembly and 3D Chromatin Architecture of Centella asiatica Insight into Evolution and Genetic Basis of Triterpenoid Saponin Biosynthesis

Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a T2T C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb repetitive sequences and 25,200 protein-coding genes. Comparative genomic analyses revealed C. asiatica is a basal lineage in the Apiaceae family with a unique single whole-genome duplication (WGD) event (Ks = 0.735) after the ancient γ-triplication, contrasting with other Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω, Ks = 0.32-0.468 and 0.835-0.956). We further constructed 3D chromatin structures (A/B compartments and TADs) in C. asiatica leaves, elucidating the influence of chromatin organization on WGD gene expression. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production, while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene co-expression network analysis (WGCNA) further highlighted the pathways modulated in response to MeJA, offering insights into the regulatory networks governing saponin synthesis. This work not only provides a valuable genomic resource for C. asiatica but also shed light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites