Scientists decode the survival secrets of a rare Chinese maple
image: Photographs of A. pentaphyllum. (a) Adult tree. (b) Massive distribution along the Yalong River valley. (c) Flower. (d) Samara. (e) Seedling. (f) (g) Leaves in different colors during autumn.
Credit: Horticulture Research
Acer pentaphyllum—a striking maple native to the Yalong River valley in Sichuan, China—was once thought to be extinct. Known for its narrow, five-lobed leaves and brilliant autumn colors, this species has become critically endangered due to habitat fragmentation, overgrazing, and road construction. Its restricted distribution and small isolated populations make it highly vulnerable to climate change and human disturbances. Despite its ornamental and scientific value, the lack of genomic data has long hindered conservation efforts. Due to these challenges, there is an urgent need to investigate its genetic basis of adaptation and population decline through integrative genomic research.
Researchers from the Chengdu Institute of Biology, Chinese Academy of Sciences, and their collaborators have decoded the complete genome of Acer pentaphyllum, marking a milestone in plant conservation genomics. The study (DOI: 10.1093/hr/uhae357), published on April 1, 2025 in Horticulture Research, provides a comprehensive genomic and population-level analysis of 227 individuals from 28 wild populations. Using PacBio HiFi and Hi-C sequencing technologies, the team revealed the species’ evolutionary history, adaptive mechanisms, and conservation needs for this rare maple inhabiting the dry-hot valleys of the Hengduan Mountains.
The researchers assembled a 626-megabase chromosome-level genome containing 38,540 protein-coding genes and over 70% repetitive sequences. Comparative genomic analyses showed rapid amplification of long terminal repeat retrotransposons (LTR-RTs) during the past 10 million years—coinciding with the uplift of the Hengduan Mountains and dramatic climate changes. Gene family expansions linked to photosynthesis, hormone signaling, and stress response likely enhanced the species’ adaptation to high temperature and drought.
Population resequencing of 227 samples revealed alarmingly low genetic diversity (π = 1.04 × 10⁻³), extensive inbreeding, and accumulation of deleterious mutations, especially in small and isolated edge populations such as TKX and CDG. Historical reconstruction suggested two major population bottlenecks during the Pleistocene, with a recent northward contraction of suitable habitats. The study further identified distinct genetic clusters corresponding to geographic regions and proposed several evolutionarily significant units (ESUs) for targeted conservation management. Together, these findings illustrate how climatic shifts and human disturbances have shaped the species’ current genetic landscape and endangered status.
“Our genomic analyses revealed that Acer pentaphyllum has undergone a long evolutionary struggle for survival,” said corresponding author Bo Xu, from the Chengdu Institute of Biology, Chinese Academy of Sciences. “The species’ low genetic diversity and high inbreeding highlight an urgent need for intervention. By combining genomics and field surveys, we can now design evidence-based conservation strategies, such as identifying management units and implementing genetic rescue programs. This genome provides a critical foundation for conserving A. pentaphyllum and other plants adapted to extreme environments.”
The genomic insights from this study will guide practical actions for preserving Acer pentaphyllum through habitat protection, restoration, and assisted gene flow. Populations with higher genetic diversity, such as those in central Yalong River regions, could serve as donor sources for genetic rescue of small, inbred populations. The reference genome also offers a valuable resource for horticultural breeding, enabling the development of drought-tolerant ornamental maples. Beyond species conservation, this work provides a model for studying plant adaptation to arid mountain ecosystems and the genomic impacts of climate change on narrowly distributed species.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae357
Funding information
This work was supported by the National Natural Science Foundation of China (NSFC Grant No. 32400304), the Wild Plants Sharing and Service Platform of Sichuan Province, and the Western China Youth Scholars Project.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2024. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.