Phylogenomics and Molecular Evolution: Integrating Genomic Data to Understand Plant Diversity and Adaptation

Recent advances in high-throughput sequencing and bioinformatics have revolutionized plant evolutionary research, enabling genome-scale analyses to address long-standing questions in systematics, diversification, and adaptation. Phylogenomics integrates large genomic datasets from chloroplast, nuclear, and mitochondrial genomes to reconstruct robust evolutionary relationships across plant lineages. Among these, chloroplast genomes have played a central role due to their conserved structure, uniparental inheritance, and suitability for resolving phylogenetic relationships at multiple taxonomic levels. However, submissions focused primarily on generating organellar genome sequences without substantive evolutionary inference, robust comparative context, or clear integration within broader phylogenomic questions are unlikely to be considered. Molecular evolutionary analyses further allow the identification of selective pressures, genome structural variation, and lineage-specific adaptations shaped by ecological and environmental factors. Despite the rapid growth of plant genomic resources, many taxa and ecosystems remain underrepresented, limiting comprehensive evolutionary interpretations. This Research Topic provides a focused platform to integrate genomic data and evolutionary approaches to better understand plant diversity and adaptive evolution.

The rapid expansion of plant genomic data has created unprecedented opportunities to investigate evolutionary relationships, genome evolution, and adaptive processes across plant lineages. However, many studies remain fragmented, focusing on single markers or limited taxa, resulting in unresolved phylogenetic relationships and an incomplete understanding of the molecular mechanisms underlying plant diversity and adaptation. In particular, the integration of chloroplast genomic data with broader phylogenomic and molecular evolutionary frameworks remains underutilized for many plant groups. The goal of this Research Topic is to address these gaps by promoting integrative research that combines genome-scale data with phylogenetic and evolutionary analyses. This collection aims to encourage studies that leverage chloroplast, nuclear, and mitochondrial genomes to resolve complex evolutionary histories, identify signatures of selection, and link genomic variation to ecological and adaptive traits. By fostering interdisciplinary and comparative approaches, this Research Topic seeks to advance a comprehensive understanding of plant diversity, evolution, and adaptation within phytoecosystems.

This Research Topic welcomes high-quality contributions that apply phylogenomic and molecular evolutionary approaches to understand plant diversity, evolutionary relationships, and adaptation. We invite studies focusing on comparative plastome analysis and genome structural evolution, as well as integrative analyses combining chloroplast, nuclear, and mitochondrial genomic data. Submissions limited to organellar genome sequencing/assembly and descriptive annotation, without clear evolutionary novelty or integrative analyses, will be considered out of scope and may be declined at initial assessment. Contributions addressing phylogenetic reconstruction, molecular dating, adaptive evolution, and signatures of selection in plant genomes are particularly encouraged. The scope also includes applications of genomic data in plant systematics, taxonomy, conservation genetics, and phytoecosystem research. Studies linking genomic variation with ecological, biogeographical, or functional traits are especially welcome. This Research Topic accepts Original Research articles, Reviews, and Mini-Reviews that provide novel insights, methodological advances, or comprehensive syntheses relevant to plant phylogenomics and molecular evolution.