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

This dataset contains comprehensive mitochondrial and plastid genomic data for 58 angiosperm species (57 angiosperms + 1 gymnosperm outgroup) used to investigate deep phylogenetic relationships among major angiosperm lineages. The repository includes:1. Raw Gene Sequences: Original FASTA sequences for 29 mitochondrial and 73 plastid protein-coding genes extracted from 58 species, including two newly assembled genomes (Ceratophyllum demersum and Chloranthus sessilifolius).2. Concatenated Alignment Matrices: Eight supermatrix alignments representing different data types (complete CDS, amino acids, codon12, RNA-edited sequences, and RNA-editing-site-deleted sequences) for both mitochondrial and plastid datasets. These files serve as direct inputs for phylogenetic inference.3. Phylogenetic Trees: A comprehensive collection of 31 mitochondrial trees (20 from full dataset analyses + 11 from optimal gene set analyses), 11 plastid trees, and 29 individual mitochondrial gene 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 (https://github.com/Liyun-Nie/mtAPG.git and https://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.