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

doi:10.1016/j.pld.2025.09.004

Plant Diversity ›› 2026, Vol. 48 ›› Issue (02): 246-261.DOI: 10.1016/j.pld.2025.09.004

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

Chao Yan^a, Ming-tai An^a,b, Ming Tang^c,d, Xin-xiang Bai^a,b, Xu Xiao^a, Zhao-hui Ran^a, Zhi Li^a,b

a. College of Forestry, Guizhou University, Guiyang 550025, China;
b. Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China;
c. College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China;
d. Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang 330045, China

Received:2025-04-25 Revised:2025-07-24 Online:2026-05-19 Published:2026-03-25
Contact: Ming Tang,E-mail:tangming@jxau.edu.cn;Zhi Li,E-mail:zli7@gzu.edu.cn
Supported by:
This work was supported by the National Natural Science Foundation of China (32400179, 31960043, 32360101), the National Key R&D Program of China (2024YFF1307400), and the 2024 Guizhou Science and Technology Innovation Talent Team Construction Project: Wildlife Innovation Team of the Forestry College of Guizhou University (Qian ke he ren cai CXTD [2025] 053).

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

Chao Yan^a, Ming-tai An^a,b, Ming Tang^c,d, Xin-xiang Bai^a,b, Xu Xiao^a, Zhao-hui Ran^a, Zhi Li^a,b

a. College of Forestry, Guizhou University, Guiyang 550025, China;
b. Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China;
c. College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China;
d. Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang 330045, China

通讯作者: Ming Tang,E-mail:tangming@jxau.edu.cn;Zhi Li,E-mail:zli7@gzu.edu.cn
基金资助:
This work was supported by the National Natural Science Foundation of China (32400179, 31960043, 32360101), the National Key R&D Program of China (2024YFF1307400), and the 2024 Guizhou Science and Technology Innovation Talent Team Construction Project: Wildlife Innovation Team of the Forestry College of Guizhou University (Qian ke he ren cai CXTD [2025] 053).

Abstract

Abstract: 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.

Key words: Camellia rubituberculata, Endemic species, Genome assembly, Karst adaptation, Population genetics

摘要： 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.

关键词: Camellia rubituberculata, Endemic species, Genome assembly, Karst adaptation, Population genetics

Chao Yan, Ming-tai An, Ming Tang, Xin-xiang Bai, Xu Xiao, Zhao-hui Ran, Zhi Li. Chromosome-level genome assembly and population genomics analysis of Camellia rubituberculata provide insights into adaptation to karst habitats[J]. Plant Diversity, 2026, 48(02): 246-261.

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

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

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