Plant genome evolution: From genomic variation to environmental adaptation

Adaptive evolution contributes to species diversification and reproductive success, which is a central focus of evolutionary biology. Elucidating the underlying mechanisms is crucial for understanding how plants respond to changing environments. Recent sequencing advances have generated vast plant genomic data, enabling evolutionary analyses at unprecedented phylogenetic depth and molecular resolution. Here, we survey the landscape of sequenced plant genomes, summarize recent advances in sequencing technologies and assembly methods, and synthesize how genomic variants are detected through micro- and macro-evolutionary analyses and how their fates are shaped by distinct modes of selection. We then highlight several major forms of genomic variation and their potential contributions to adaptive evolution, including structural variants, transposable element activity, and whole-genome duplications. We further survey the associated genomic signatures of extremophiles and plant terrestrialization as frameworks for understanding diverse and compound environmental stresses. Finally, we discuss emerging genomic research trends and future directions, which aim to deepen insights into the evolutionary architecture of plant genomes and provide a theoretical foundation for crop improvement, ecological conservation, and biotechnological applications.