Genetic diversity and differentiation characteristics of the widespread plant Phragmites australis in eastern China

Introduction Phragmites australis (common reed) is a globally distributed and highly productive emergent macrophyte with important ecological functions in wetland ecosystems. However, the genetic diversity and population differentiation of P. australis in eastern China remain insufficiently characterized. Methods In this study, we performed RAD-seq-based reduced-representation genome sequencing of 98 P. australis individuals collected from populations distributed across eastern China to characterize genetic variation, population structure, and geographic differentiation among populations. Results A total of 730,413 high-quality single-nucleotide polymorphisms (SNPs) were identified. Population genomic analyses revealed relatively high genetic diversity across eastern Chinese populations and substantial population structure, with the broad geographic distribution of P. australis associated with the formation of multiple genetic clusters. Functional enrichment analyses further indicated that pathways related to plant–pathogen interactions and sugar metabolism, highlighting potential biological processes associated with the genetic variation observed among the sampled populations. Among the sampled populations, the Longqi Bay (LQW) population exhibited the most distinct genetic characteristics, followed by the Baiyangdian Lake (BYD) and Xizhi Lake (XZH) populations. In contrast, the Weishan Lake (WSH) and Panjin (PJ) populations showed relatively low genetic differentiation and displayed genomic variation patterns more similar to those of the reference genome. Notably, the Yangtze River region coincided with a pronounced north–south transition in genetic structure. Discussion Overall, these findings provide new insights into the population genetic structure, evolutionary history, and geographic differentiation of P. australis in eastern China and provide valuable genomic resources for investigating its evolutionary dynamics and ecological adaptation.