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

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.