Raw fasta, alignments and trees files used in mito-APG analysis

Reconstructing the phylogenetic relationships among the five major angiosperm clades remains a formidable challenge, as large-scale nuclear and plastid datasets often yield inconsistent frameworks. To evaluate the utility of mitochondrial genomes in resolving these relationships, we assembled the first complete mitochondrial genomes for <i>Ceratophyllum</i> and <i>Chloranthus</i>, thereby filling a critical genomic data gap for key lineages. We constructed five mitochondrial datasets (CDS, protein, codon12, C-to-U edited, and C-to-U deleted CDS) along with three plastid datasets (CDS, protein, and codon12) and employed diverse phylogenetic reconstruction methods (concatenation and coalescent approaches) with various models. Our analyses revealed significant topological conflicts between mitochondrial and plastid phylogenies. Specifically, mitochondrial trees consistently supported a sister-group relationship between <i>Ceratophyllum</i> and <i>Chloranthus</i>, and more than half of the mitochondrial datasets resolved eudicots and monocots as sister groups, whereas plastid trees displayed greater consistency. Notably, editing or deleting RNA editing sites from mitochondrial sequences increased tree stability. Widespread gene-tree heterogeneity was observed, with high-conflict genes tending to have lower sequence entropy and shorter lengths—suggesting that insufficient phylogenetic signal, rather than slow evolution rates, is the primary source of conflict.