High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies

Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to dry-hot valleys of the Yalong River in western Sichuan, China, requires urgent conservation efforts due to its extremely rarity and restricted distribution. In this study, we present a high-quality chromosome-level reference genome of A. pentaphyllum (626 Mb, 2n = 26), comprising 70.64% repetitive sequences and 38,540 protein-coding genes. Phylogenetic analysis shows that A. pentaphyllum diverged from a clade consisting of A. yangbiense and A. saccharum in the late Eocene (∼37.83 Ma). In the genome of A. pentaphyllum , genes involved in responding to external environmental change have undergone expansion and positive selection, potentially reflecting its adaptive strategies. While no recent independent whole-genome duplication events were detected, a recent rapid amplification of transposable elements was observed. 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 upstream colonization along the Yalong River, with two severe population bottlenecks correlating with major Pleistocene climatic transitions. In addition, most populations exhibit high inbreeding and genetic load, particularly those at range edges (TKX, CDG, TES). Based on these genomic insights, we propose targeted conservation strategies, including genetic rescue measures, to safeguard this unique maple species. These findings not only contribute to the preservation of A. pentaphyllum but also enhance our understanding of plant adaptation to extreme environments and the impacts of climate change on species with restricted distributions.