A telomere-to-telomere genome assembly of Asparagus cochinchinensis reveals the evolution of centromere and steroidal saponin biosynthesis

Abstract Asparagus cochinchinensis is a perennial medicinal plant that accumulates bioactive steroidal saponins in enlarged tuberous roots, yet the genomic basis of its specialized metabolism and the regulatory mechanisms underlying steroidal saponin biosynthesis remain poorly understood. Here, we present the first telomere-to-telomere genome assembly for this species, generated by integrating PacBio HiFi, Oxford Nanopore Technologies, and Hi-C data. The ~ 1.50-Gb assembly revealed uniformly organized centromeres, where tandem repeats and Gypsy retrotransposons are evenly distributed across megabase-scale domains—a pattern appears to contrast with the heterogeneous architecture commonly observed in sexually reproducing plants, potentially reflecting an adaptation associated with its vegetative propagation lifestyle. Comparative genomic analyses uncovered an ancient whole-genome duplication shared across the genus Asparagus, together with lineage-specific expansion of gene families involved in specialized metabolism. Notably, we identified a nine-gene UDP-glycosyltransferase cluster on Chr05 implicated in steroidal saponin biosynthesis, six of which showed tuber-specific expression. This cluster is activated by the Myb67 transcription factor. Together, this T2T genome provides a foundational resource for Asparagus genomics, illuminating both centromere evolution and the genomic basis of steroidal saponin biosynthesis.