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.
The "Tropical-Temperate Integration" strategy, which involves the introgression of robust stress resistance from tropical germplasm into elite temperate lines, is a genomic imperative for stabilizing maize yields under climate change. Here, we investigated the genomic architecture of this strategy using KNY8009, a representative elite hybrid of the Huang-Huai-Hai summer maize region, by generating platinum-quality, pedigree-resolved genome assemblies across its lineage. We identified massive knob180 tandem repeat arrays as primary drivers of maize genome size plasticity and as hotspots for organellar DNA capture, while also demonstrating that these regions were a major source of error in reference-guided scaffolding. Furthermore, we identified hyperdivergent regions (HDRs) as punctate hotspots of extreme genetic diversity, whose boundaries were enriched for known regulatory motifs. Intensive functional genomics and novel genome-wide association studies across 38 traits confirm that targeted tropical introgressions reshaped specific genomic landscapes, conferring broad-spectrum resistance while preserving the elite temperate backbone. Finally, an alignment-free k-mer analysis provided an unbiased atlas of tropical-temperate divergence, valuable for further integration. Our study elucidated the genetic basis of Tropical-Temperate Integration, and established a rigorous, structural-aware framework for decoding the hidden variations that drive modern crop improvement.
