Chromosome-level genome assembly and population genomics analysis of Camellia rubituberculata provide insights into adaptation to karst habitats

Karst flora confined to isolated ‘habitat islands’ evolve specialized adaptations and unique traits, serving as ideal models for investigating adaptive evolution and species diversification mechanisms. Camellia rubituberculata , endemic to the karst habitats of Guizhou, China, can serve as a model for adaptive evolution and diversity in karst-endemic woody species. However, the lack of a chromosome-level genome for this species has limited in-depth studies on its adaptations to karst and posed a barrier to its genetic improvement. In this study, a chromosome-level genome assembly of C. rubituberculata was generated, with 15 pseudo-chromosomes and a genome size of 2.50 Gb (scaffold N50 = 168.34 Mb, 55,302 protein-coding genes). Comparative genomics revealed two whole-genome duplications (WGDs), namely, an ancient γ-event (∼120 Mya) and a subsequent genus-wide event (∼86 Mya), after which gene families linked to karst adaptation (e.g., photosynthesis) were significantly expanded. Selective sweep analysis showed that selected genes were associated with phytohormone transmission and metabolism. Genes functionally annotated as involved in stress responses—including SAUR, BSK, NCL, CDPK, and NDPK—participate in calcium homeostasis and ion transport pathways under karst-specific stresses. MYB transcription factors, which are crucial in plant responses to stresses, including drought, may be key for adaptation to the high salinity and drought stress in karst environments. The divergent selection in wild and cultivated groups highlight key adaptations in plant hormone transduction and calcium transport. By elucidating karst adaptation in C. rubituberculata , this work establishes essential genomic resources for advancing genetic evolution research and molecular breeding across Camellia species. • Assembled chromosome-level genomes of Camellia species grown in karst habitats • Genome mapping reveals the structure and genetic make-up of chromosomes • Discovery of two genome duplication events reveals secrets of adaptive evolution • Calcium balance-regulating gene doubles salt and drought tolerance • Resistance gene pool provides genetic blueprint for breeding and conservation of Camellia rubituberculata