Mountain ecosystems exhibit significant biodiversity, yet the genetic mechanisms that enable adaptation to severe alpine conditions remain poorly understood. Bergenia purpurascens (Saxifragaceae), a notable alpine endemic species from the Himalaya-Hengduan Mountains (HHM), serves as both a medicinal source and an ornamental plant.
This research produced a high-quality genome assembly consisting of scaffolds for 17 chromosomes, totaling 650.70 Mb and a scaffold N50 of 34.19 Mb. The study identified 45,841 protein-coding genes and 10,797 noncoding RNAs, with repeat sequences constituting 56.72% of the genome. The reference genome of B. purpurascens is a crucial resource for exploring bergenin biosynthesis and understanding plant adaptation to alpine environments.
Alpine flora must endure extreme conditions, such as low temperatures, high UV radiation, dryness, and limited growing seasons. Genomic investigations of non-model alpine species have shed light on the genetic adaptations to these harsh settings. For example, studies on two species from the Crucihimalaya genus (C. lasiocarpa and C. himalaica, Brassicaceae) on the Tibetan Plateau revealed significant expansions in gene families associated with alpine adaptation since the genus's inception. Additionally, comparisons between alpine and lower-elevation species identified positively selected genes linked to alpine adaptation, alongside convergent contractions in disease resistance-related gene families in alpine plants.
The HHM region hosts some of the highest peaks globally and is rich in alpine flora. Bergenia Moench, comprising ten species, is primarily found in the HHM and Central Asia. The rhizomes of Bergenia are the main source of bergenin, a medicinal compound used for respiratory ailments and stomach issues. B. purpurascens is endemic to the HHM, thriving at altitudes ranging from 2700 to 4800 m a.s.l. It faces heightened vulnerability to climate change compared to its lower-altitude relatives. Observations indicate that B. purpurascens is at risk of local extinction due to climate change and overexploitation for medicinal use, making it an ideal candidate for studying genetic adaptation in alpine plants.
This study integrated Illumina sequencing, Pacific Bioscience circular consensus sequencing (CCS), and high-throughput chromosome conformation capture (Hi-C) sequencing to assemble a high-quality chromosome-level genome of B. purpurascens. The resulting genome assembly spans approximately 650.70 Mb, with a scaffold N50 of 34.19 Mb. A total of 93.43% of the sequences were anchored to 17 pseudo-chromosomes. Bergenia shares a chromosome number (2n = 2x = 34) with its relatives Astilboides, Darmera, and Mukdenia.
Comparative genomic analyses were conducted on the B. purpurascens genome alongside 11 other flowering plant genomes to investigate gene evolution. The high-quality chromosome-level genome assembly of this valuable medicinal and ornamental alpine plant enhances the understanding of bergenin's biosynthetic pathway, the genetic basis of adaptation to alpine environments, and the sustainable conservation and utilization of this genetic resource.