The Cucurbita ficifolia Mitochondrial Genome: Repeat-Rich Architecture, Plastid Homology, and Synteny Turnover Across Cucurbitaceae

Abstract

Background: Cucurbita ficifolia (figleaf gourd) is an agriculturally useful cucurbit germplasm and rootstock, but its mitochondrial genome has not been examined in a comparative family-level framework. We aimed to characterize its mitochondrial reference sequence and evaluate coding composition, repetitive DNA, plastid homology, bioinformatic RNA-editing predictions, phylogenetic placement, and genome-scale synteny. Methods: PacBio Revio sequencing generated 933,158 high-fidelity (HiFi) reads totaling 14.294 Gb, with a read N50 of 15.6 kb. The 784,544-bp mitochondrial reference (GenBank accession PZ823090) was assembled with Oatk and evaluated using graph topology, competitive read-back, and junction-spanning alignments. Codon usage, repeats, mitochondrial–plastid homologous regions, bioinformatic C-to-U RNA-editing predictions, conserved-gene phylogeny, and whole-mitogenome synteny were analyzed. Results: The reference had 43.09% GC content and contained 38 distinct protein-coding genes represented by 42 loci, 26 tRNA types represented by 37 loci, and three rRNAs. Competitive read-back retained 40,971 primary mitochondrial alignments (MAPQ ≥ 20), yielding a mean depth of 547.26× and 100% breadth at ≥100×. The terminal-to-start adjacency was supported by 366 HiFi reads with ≥2-kb anchors on each side. We identified 322 simple-sequence repeats, 115 tandem repeats, and 2374 dispersed repeat pairs. For the largest 392-bp direct repeat, the two native junctions were supported by 268 and 308 reads, whereas the two reciprocal junctions were supported by one and zero reads. Ninety-one significant plastid matches collapsed to 73 mitochondrial loci and covered 74,784 unique mitochondrial bases (9.53%). Deepred-Mt generated 494 bioinformatic C-to-U RNA-editing predictions in 37 genes, and phylogenomics placed C. ficifolia as sister to the C. pepo–C. maxima pair with maximal support despite extensive synteny turnover. Conclusions: The C. ficifolia mitogenome combines a conserved coding repertoire with abundant short repeats, appreciable plastid homology, and extensive rearrangement. Read evidence supports the submitted terminal-to-start adjacency but does not establish a unique or predominant circular molecule in vivo; likewise, the largest repeat showed no robust reciprocal-junction signal. All RNA-editing sites reported here are bioinformatic predictions rather than transcript–validated events.