Systematic Phylogenomics: Reconstructing the Tree of Life in the Genomic Era

Plant systematics has transitioned from a discipline based primarily on morphology and single-gene sequences to "Phylogenomics", utilizing whole-genome and transcriptomic data. This paper explores the evolutionary history of land plants (Embryophytes), focusing on the critical transitions from bryophytes to tracheophytes and the explosive radiation of angiosperms during the Cretaceous. We discuss the impact of Whole Genome Duplication (WGD) events on plant diversification and the resolution of long-standing "recalcitrant" nodes in the Tree of Life using High-Throughput Sequencing (HTS). Special attention is given to the APG IV (Angiosperm Phylogeny Group) system and the emerging use of Artificial Intelligence in automated botanical identification and phylogenetic mapping.