Mitochondrial and Plastid Phylogenomic Dataset for Angiosperm Deep Phylogeny: Sequence Alignments, Gene Trees, and Species Trees

These trees were inferred using Maximum Likelihood and Bayesian methods with partitioned and non-partitioned models.4. Metadata: Species information, lineage assignments, and accession numbers for all sampled taxa.This dataset was generated using standardized pipelines for genome annotation, sequence alignment (MAFFT/MACSE), alignment trimming (Gblocks), and phylogenetic inference (IQ-TREE/MrBayes). The data support all phylogenetic analyses and conclusions reported in the associated manuscript, including the novel PhyloForensics framework for identifying phylogenetically stable genes.All analysis scripts and detailed workflows are available at GitHub (github.com/Liyun-Nie/mtAPG.git and github.com/Liyun-Nie/PhyloForensics).

This dataset enables full reproducibility of the published analyses and provides a foundation for future comparative phylogenomic studies in angiosperms.