Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

doi:10.1016/j.pld.2025.06.006

Plant Diversity ›› 2025, Vol. 47 ›› Issue (05): 746-758.DOI: 10.1016/j.pld.2025.06.006

• Articles • Previous Articles Next Articles

Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

Nana Peng (彭娜娜)^a,b,c, Lihua Yang (杨丽华)^a,c, Xizuo Shi (史习佐)^a,b,c, Hanghui Kong (孔航辉)^a,c, Ming Kang (康明)^a,c

a. State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China

Received:2025-02-18 Revised:2025-06-17 Online:2025-09-29 Published:2025-09-29
Contact: Ming Kang,E-mail:mingkang@scbg.ac.cn
Supported by:
This work was supported by National Key R&D Program of China (2024YFF1307400) and Guangdong S&T Program (2022B1111230001).

Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

Nana Peng (彭娜娜)^a,b,c, Lihua Yang (杨丽华)^a,c, Xizuo Shi (史习佐)^a,b,c, Hanghui Kong (孔航辉)^a,c, Ming Kang (康明)^a,c

a. State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China;
c. Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China

通讯作者: Ming Kang,E-mail:mingkang@scbg.ac.cn
基金资助:
This work was supported by National Key R&D Program of China (2024YFF1307400) and Guangdong S&T Program (2022B1111230001).

Abstract

Abstract: Preserving genetic diversity is crucial for the long-term survival of wild plant species, yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation. Here, we present a comparative genomic study of the critically endangered Oreocharis esquirolii (Gesneriaceae) and its widespread congener O. maximowiczii. We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O. esquirolii and 79 O. maximowiczii individuals. Our analyses reveal substantially lower genetic diversity and higher inbreeding in O. esquirolii, despite its overall reduced mutational burden. Notably, O. esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O. maximowiczii, suggesting that limited opportunities for purging have allowed these variants to accumulate. These contrasting genomic profiles likely reflect divergent demographic histories, with O. esquirolii having experienced severe bottlenecks and protracted population decline. Collectively, our findings highlight the critically endangered status of O. esquirolii, characterized by diminished genetic diversity, pronounced inbreeding, and reduced ability to eliminate deleterious alleles. This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures, including habitat protection and ex situ preservation efforts, to mitigate the extinction risk facing O. esquirolii and potentially other threatened congeners.

Key words: Conservation genomics, Demographic history, Genetic diversity, Mutation load, Oreocharis esquirolii

摘要： Preserving genetic diversity is crucial for the long-term survival of wild plant species, yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation. Here, we present a comparative genomic study of the critically endangered Oreocharis esquirolii (Gesneriaceae) and its widespread congener O. maximowiczii. We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O. esquirolii and 79 O. maximowiczii individuals. Our analyses reveal substantially lower genetic diversity and higher inbreeding in O. esquirolii, despite its overall reduced mutational burden. Notably, O. esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O. maximowiczii, suggesting that limited opportunities for purging have allowed these variants to accumulate. These contrasting genomic profiles likely reflect divergent demographic histories, with O. esquirolii having experienced severe bottlenecks and protracted population decline. Collectively, our findings highlight the critically endangered status of O. esquirolii, characterized by diminished genetic diversity, pronounced inbreeding, and reduced ability to eliminate deleterious alleles. This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures, including habitat protection and ex situ preservation efforts, to mitigate the extinction risk facing O. esquirolii and potentially other threatened congeners.

关键词: Conservation genomics, Demographic history, Genetic diversity, Mutation load, Oreocharis esquirolii

Nana Peng (彭娜娜), Lihua Yang (杨丽华), Xizuo Shi (史习佐), Hanghui Kong (孔航辉), Ming Kang (康明). Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species[J]. Plant Diversity, 2025, 47(05): 746-758.

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Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

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