Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii

doi:10.1016/j.pld.2026.03.001

Plant Diversity ›› 2026, Vol. 48 ›› Issue (03): 487-500.DOI: 10.1016/j.pld.2026.03.001

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Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii

Jiaxin Li^a,b,c, Lihua Yang^a,c, Danqi Li^d, Chen Feng^d, Ming Kang^a,b,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;
d Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China

Received:2025-11-28 Revised:2026-03-02 Online:2026-06-10 Published:2026-05-25
Contact: Chen Feng,E-mail:fengc@lsbg.cn;Ming Kang,E-mail:mingkang@scbg.ac.cn
Supported by:
This work was supported by the Guangdong S&T Program (2022B1111230001) and National Key R&D Program of China (2024YFF1307400).

Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii

Jiaxin Li^a,b,c, Lihua Yang^a,c, Danqi Li^d, Chen Feng^d, Ming Kang^a,b,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;
d Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China

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

Abstract

Abstract: Relict trees are key to understanding macroevolution, biogeography, and extinction risk under environmental change, yet genome-wide data on diversity and demography remain scarce. Perkinsiodendron macgregorii, a monotypic East Asian relict within Styracaceae, is of notable horticultural and conservation significance. Here, we assembled a chromosome-level genome (~1.15 Gb) and resequenced 167 individuals from 30 populations across its range. We performed a comparative analysis of single nucleotide polymorphisms (SNPs) and structural variants (SVs) to assess population structure, mutation load, climate-associated variation, and genomic vulnerability. Both SNP and SV datasets consistently resolved two evolutionarily cohesive lineages broadly separated by the Wuyi Mountains. Demographic reconstructions dated East-West divergence to ~0.16 Ma and revealed a long-term decline in effective population size (N_e) since the Late Pleistocene, with lineage-specific fluctuations through the Quaternary. Genome-wide diversity was moderate overall, but the West lineage showed elevated inbreeding and realized genetic load. Relative to SNPs, SVs showed higher proportions of HIGH-impact mutations (i.e., variants more likely to disrupt gene function), consistent with the larger genomic span of SVs and their greater potential deleterious effects. Functional enrichment of core adaptive variants (755 SNPs, 63 SVs) revealed divergent adaptive signals across marker classes. Genomic offset and RONA projections were concordant and highlighted western Jiangxi and southwestern Hunan as future vulnerability hotspots, with risk increasing under higher-emissions scenarios. Together, these results support recognizing East and West lineages as primary conservation units and prioritizing at-risk West populations (JXJGS, HNSHS) for management, while safeguarding genetically distinctive populations (e.g., JXGS, JXYJF) as secondary units to preserve evolutionary potential.

Key words: Demographic history, Genetic load, Genomic vulnerability, Perkinsiodendron macgregorii, Relict tree, Structural variants

摘要： Relict trees are key to understanding macroevolution, biogeography, and extinction risk under environmental change, yet genome-wide data on diversity and demography remain scarce. Perkinsiodendron macgregorii, a monotypic East Asian relict within Styracaceae, is of notable horticultural and conservation significance. Here, we assembled a chromosome-level genome (~1.15 Gb) and resequenced 167 individuals from 30 populations across its range. We performed a comparative analysis of single nucleotide polymorphisms (SNPs) and structural variants (SVs) to assess population structure, mutation load, climate-associated variation, and genomic vulnerability. Both SNP and SV datasets consistently resolved two evolutionarily cohesive lineages broadly separated by the Wuyi Mountains. Demographic reconstructions dated East-West divergence to ~0.16 Ma and revealed a long-term decline in effective population size (N_e) since the Late Pleistocene, with lineage-specific fluctuations through the Quaternary. Genome-wide diversity was moderate overall, but the West lineage showed elevated inbreeding and realized genetic load. Relative to SNPs, SVs showed higher proportions of HIGH-impact mutations (i.e., variants more likely to disrupt gene function), consistent with the larger genomic span of SVs and their greater potential deleterious effects. Functional enrichment of core adaptive variants (755 SNPs, 63 SVs) revealed divergent adaptive signals across marker classes. Genomic offset and RONA projections were concordant and highlighted western Jiangxi and southwestern Hunan as future vulnerability hotspots, with risk increasing under higher-emissions scenarios. Together, these results support recognizing East and West lineages as primary conservation units and prioritizing at-risk West populations (JXJGS, HNSHS) for management, while safeguarding genetically distinctive populations (e.g., JXGS, JXYJF) as secondary units to preserve evolutionary potential.

关键词: Demographic history, Genetic load, Genomic vulnerability, Perkinsiodendron macgregorii, Relict tree, Structural variants

Jiaxin Li, Lihua Yang, Danqi Li, Chen Feng, Ming Kang. Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii[J]. Plant Diversity, 2026, 48(03): 487-500.

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Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii

Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict tree Perkinsiodendron macgregorii

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