Genomic Insights into Adaptation of Lagerstroemia suprareticulata to Limestone Karst Habitats

Lagerstroemia suprareticulata, an endemic ornamental species in limestone karst ecosystems of Guangxi—a global biodiversity hotspot—holds significant ecological value. However, habitat degradation and anthropogenic pressures have driven this species to the brink of extinction, leading to its classification as Endangered (EN) on the China Biodiversity Red List. To address this crisis, we conducted whole-genome resequencing to generate single-nucleotide polymorphisms (SNPs) for comprehensive analyses of genetic diversity, population structure, demographic history, and adaptive variation. Our results reveal four distinct genetic clusters in L. suprareticulata, all of which share a history of population expansion followed by contraction. Maximum entropy modeling (MaxEnt) projects a severe contraction in the range under high-carbon-emission scenarios. Selective sweep analysis identified genomic regions under positive selection, including those associated with protein homeostasis, metabolism, signal transduction, and developmental regulation. Genotype–environment association (GEA) analysis further identified adaptive SNPs linked to temperature and precipitation, which were enriched in genes regulating transmembrane transport, stress response, and the immune system. Additionally, risk of non-adaptedness (RONA) analysis identified high-risk populations. By integrating genomic data with advanced analytical approaches, this study enhances our understanding of the adaptive mechanisms of L. suprareticulata to limestone karst habitats and provides critical insights for its conservation.