<b>Phylogenomics and Mitogenomic Architecture of Cucurbitaceae: Insights from Sequence Analysis​</b>

<p dir="ltr">Putatively orthologous mitochondrial protein-coding genes (PCGs) shared among all taxa were identified using PhyloSuite v1.2.2. The taxon sampling comprised both newly assembled and publicly available sequences. After removing paralogous sequences, coding DNA sequences (CDSs) were extracted. To maintain correct reading frames and preserve evolutionary signal, the nucleotide sequences were translated into amino acids, aligned with MAFFT v7.313 under the “-auto” strategy, and then back-translated to generate codon-aligned nucleotide alignments. The nucleotide alignments were further refined with Gblocks v0.91b using relaxed parameters to minimize ambiguous alignment regions while retaining phylogenetic information: minimum number of sequences for conserved/flanking positions was set to 85% of all taxa, maximum number of contiguous nonconserved positions was 8, minimum block length was 10, and gap positions were allowed “with half”. Maximum likelihood phylogenies were reconstructed with IQ-TREE v1.6.8 under the “-m MFP” option and assessed with 50,000 ultrafast bootstrap (UFBoot) replicates and 1,000 SH-like approximate likelihood ratio test (SH-aLRT) replicates. Branches with UFBoot ≥ 95% and SH-aLRT ≥ 80% were considered strongly supported. The final trees were visualized using Interactive Tree of Life (iTOL) v6.</p>