High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

doi:10.1016/j.pld.2025.11.001

Plant Diversity ›› 2026, Vol. 48 ›› Issue (02): 262-277.DOI: 10.1016/j.pld.2025.11.001

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High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

Temur Asatulloev^a,b,c, Lei Cai^a, Ziyoviddin Yusupov^c, Kai-Hua Jia^d, Ren-Gang Zhang^a,b, Komiljon Sh. Tojibaev^c, Wei-Bang Sun^a

a. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Institute of Botany, Academy of Sciences, Tashkent 100125, Uzbekistan;
d. Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources, National Saline-Alkali Tolerant Crop Germplasm Resources Nursery (Dongying), Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China

Received:2025-06-05 Revised:2025-11-03 Online:2026-05-19 Published:2026-03-25
Contact: Lei Cai,E-mail:cailei@mail.kib.ac.cn;Komiljon Sh. Tojibaev,E-mail:ktojibaev@mail.ru;Wei-Bang Sun,E-mail:wbsun@mail.kib.ac.cn
Supported by:
This work was equally supported by the National Key R&D Program of China (Grant No. 2024YFF1307400) and Yunnan Key R&D Program (Grant No. 202403AC100028), Yunnan Fundamental Research Projects (Grant No. 202301AT070318) and Yunnan Revitalization Talent Support Program “Young Talent” Projiect. We thank Dr. Yang Liu, Dr. Shi-Wei Guo, Dr. Ji-Dong Ya, Prof. Zhi-Kun Wu, Prof. Xin-Xiang Bai, Prof. Pan Li, Mr. Sheng-Hu Tang, Mr. Jian Xu, Mr. Bo Pan and Mr. De-Ming He, for their assistance in collecting materials and providing species distribution information, and we thank Dr. Feng-Mao Yang, Dr. Yang Liu, Dr. Bishal Gurung, Dr. Yu-Hang Chang and Ms. Na–Na Peng for their help in analyzing and providing data.

High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

Temur Asatulloev^a,b,c, Lei Cai^a, Ziyoviddin Yusupov^c, Kai-Hua Jia^d, Ren-Gang Zhang^a,b, Komiljon Sh. Tojibaev^c, Wei-Bang Sun^a

a. Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Institute of Botany, Academy of Sciences, Tashkent 100125, Uzbekistan;
d. Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources, National Saline-Alkali Tolerant Crop Germplasm Resources Nursery (Dongying), Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China

通讯作者: Lei Cai,E-mail:cailei@mail.kib.ac.cn;Komiljon Sh. Tojibaev,E-mail:ktojibaev@mail.ru;Wei-Bang Sun,E-mail:wbsun@mail.kib.ac.cn
基金资助:
This work was equally supported by the National Key R&D Program of China (Grant No. 2024YFF1307400) and Yunnan Key R&D Program (Grant No. 202403AC100028), Yunnan Fundamental Research Projects (Grant No. 202301AT070318) and Yunnan Revitalization Talent Support Program “Young Talent” Projiect. We thank Dr. Yang Liu, Dr. Shi-Wei Guo, Dr. Ji-Dong Ya, Prof. Zhi-Kun Wu, Prof. Xin-Xiang Bai, Prof. Pan Li, Mr. Sheng-Hu Tang, Mr. Jian Xu, Mr. Bo Pan and Mr. De-Ming He, for their assistance in collecting materials and providing species distribution information, and we thank Dr. Feng-Mao Yang, Dr. Yang Liu, Dr. Bishal Gurung, Dr. Yu-Hang Chang and Ms. Na–Na Peng for their help in analyzing and providing data.

Abstract

Abstract: Despite the ecological importance of karst ecosystems, genomic studies on the conservation and adaptation of karst plant species, particularly threatened wild species, remain scarce. Here, we investigate the genetic architecture, demographic history, and adaptive potential of Oreocharis mileensis, a threatened karst-endemic resurrection plant. We generated a high-quality, phased genome assembly of 3.99 Gb covering two haplotypes with a contig N50 of 124 Mb, revealing three lineage-specific whole-genome duplication events following the ancestral γ event. Population resequencing of 107 individuals across 10 localities uncovered strong population structure, low gene flow, and high genetic differentiation, indicating long-term isolation. Core populations exhibited elevated inbreeding, whereas peripheral populations showed reduced runs of homozygosity and fewer deleterious mutations, suggesting historical demographic events and possible purging effects. pRDA analyses on putatively adaptive loci revealed that genetic variation is primarily aligned with pre-existing population structure. Functional annotation of putatively adaptive SNPs identified genes associated with drought tolerance and rapid recovery after rewatering. Gradient Forest models revealed substantial genomic offset in almost all populations, highlighting their increased vulnerability under projected climate scenarios. Based on these findings, we propose conservation strategies that include delineating eight genetically informed management units and facilitating assisted gene flow among compatible populations. For highly isolated populations, ex situ conservation, habitat restoration, and cultivation for horticultural use are recommended to mitigate genetic erosion and enhance adaptive resilience. This study provides critical insights into how historical, demographic, and environmental factors shape genetic diversity and informs conservation efforts for plant species in fragile karst ecosystems.

Key words: Oreocharis mileensis, Isolation by environment, Deleterious mutation, Adaptive potential, Karst region

摘要： Despite the ecological importance of karst ecosystems, genomic studies on the conservation and adaptation of karst plant species, particularly threatened wild species, remain scarce. Here, we investigate the genetic architecture, demographic history, and adaptive potential of Oreocharis mileensis, a threatened karst-endemic resurrection plant. We generated a high-quality, phased genome assembly of 3.99 Gb covering two haplotypes with a contig N50 of 124 Mb, revealing three lineage-specific whole-genome duplication events following the ancestral γ event. Population resequencing of 107 individuals across 10 localities uncovered strong population structure, low gene flow, and high genetic differentiation, indicating long-term isolation. Core populations exhibited elevated inbreeding, whereas peripheral populations showed reduced runs of homozygosity and fewer deleterious mutations, suggesting historical demographic events and possible purging effects. pRDA analyses on putatively adaptive loci revealed that genetic variation is primarily aligned with pre-existing population structure. Functional annotation of putatively adaptive SNPs identified genes associated with drought tolerance and rapid recovery after rewatering. Gradient Forest models revealed substantial genomic offset in almost all populations, highlighting their increased vulnerability under projected climate scenarios. Based on these findings, we propose conservation strategies that include delineating eight genetically informed management units and facilitating assisted gene flow among compatible populations. For highly isolated populations, ex situ conservation, habitat restoration, and cultivation for horticultural use are recommended to mitigate genetic erosion and enhance adaptive resilience. This study provides critical insights into how historical, demographic, and environmental factors shape genetic diversity and informs conservation efforts for plant species in fragile karst ecosystems.

关键词: Oreocharis mileensis, Isolation by environment, Deleterious mutation, Adaptive potential, Karst region

Temur Asatulloev, Lei Cai, Ziyoviddin Yusupov, Kai-Hua Jia, Ren-Gang Zhang, Komiljon Sh. Tojibaev, Wei-Bang Sun. High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region[J]. Plant Diversity, 2026, 48(02): 262-277.

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High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

High-quality genome of Oreocharis mileensis (Gesneriaceae) provides insights into the adaptation and conservation of highly threatened species in karst region

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