Abstract: Karst area are well known as their extremely biodiversity and the investigation of plants adaptation in these unique environments is one of research hotspots. Previous studies primarily focused on the genomic adaptation of karst endemic species, but the special adaptation of facultative species remains unclear. Hemiboea subcapitata, a traditional medicinal plant growing in both karst and non-karst areas, serves as a valuable model for understanding the genomic mechanisms of this issue. Here, the genome of H. subcapitata was sequenced using the PacBio and Illumina platforms and de novo assembled with contig N50 value of 21.11 Mb. The assembled genomic size was 763.59 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) quality value was 98.10%, and 92.87% sequences were anchored to 16 chromosomes. Comparative genome analyses identified three whole-genome duplication (WGD) events: γ-WGT event (115–130 Ma) shared by all eudicots, WGD2 shared within Lamiales except Oleaceae (67.57 Ma) and the recently independent WGD1 unique to H. subcapitata (16.92 Ma). These three WGD events likely facilitated the expansion of stress-responsive gene families, which in turn influenced functional pathway regulation. Especially, genomic and transcriptome analyses identified 25 key genes in the flavonoid pathway and candidate MYB transcription factors related to environmental adaptation. Compared to the karst-endemic Primulina tabacum, H. subcapitata showed upregulation of 25 key flavonoid pathway genes (96% in roots, 92% in leaves, 88% in flowers). This mechanism of expanding ecological niches through metabolic pathway regulation was the unique adaptive strategy of H. subcapitata. This study provides valuable data for further resource utilization and conservation of Hemiboea.

Key words: evolution, flavonoids, genomic adaptation, Hemiboea subcapitata, whole-genome duplication.