High-resolution genome assembly and population genetic study of the endangered maple Acer pentaphyllum (Sapindaceae): implications for conservation strategies

Abstract

Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species’ unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10⁻³) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of A. pentaphyllum but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments.

Acknowledgements

We thank Min Liao, Junyi Zhang, Yushan Zhou, Shuo Tan, Cier Zhongyang, and Pianchu for assistance with sample collection. We thank Yongling Qiu for her help with writing. We also gratefully thank Wentai Dai for providing transcriptome data of leaves. 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.

Author contributions

B.X. conceived the project. B.X. and Y.F. designed the research. X.L., Q.Y., H.N.D., L.S.J., Y.F., and W.B.J. collected the materials. X.L. and Y.F. analyzed the data. X.J.C. performed species distribution modeling. X.L., Y.F., B.X., and W.B.J. contributed to the interpretation of results. X.L., Y.F., and L.S.J. wrote the manuscript, B.X. and Y.F. revised the manuscript. All authors read and approved the manuscript.

Data availability

All data that support the findings of this study, including sequencing data, reference genome, and gene annotations, have been deposited into CNGB Sequence Archive (CNSA; [110]) of China National GeneBank DataBase (CNGBdb) with accession number CNP0006021 (reviewer link: http://db.cngb.org/cnsa/project/CNP0006021_715ecb62/reviewlink/).

Conflict of interests

All authors declare no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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