{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:05:06Z","timestamp":1789707906983,"version":"4.0.1"},"reference-count":55,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020443","name":"Bengbu University","doi-asserted-by":"publisher","award":["2024AH051177"],"award-info":[{"award-number":["2024AH051177"]}],"id":[{"id":"10.13039\/501100020443","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2024AH051177"],"award-info":[{"award-number":["2024AH051177"]}],"id":[{"id":"https:\/\/ror.org\/05p8d2v16","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background:\u00a0Cucurbita 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\u2013plastid 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 \u2265 20), yielding a mean depth of 547.26\u00d7 and 100% breadth at \u2265100\u00d7. The terminal-to-start adjacency was supported by 366 HiFi reads with \u22652-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\u2013C. 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\u2013validated events.<\/jats:p>","DOI":"10.3390\/genes17091103","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T17:14:59Z","timestamp":1789146899000},"page":"1103","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Cucurbita ficifolia Mitochondrial Genome: Repeat-Rich Architecture, Plastid Homology, and Synteny Turnover Across Cucurbitaceae"],"prefix":"10.3390","volume":"17","author":[{"given":"Jun","family":"Yang","sequence":"first","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinhui","family":"Li","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huilin","family":"Cheng","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingfeng","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weifan","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Lu","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengcheng","family":"Ling","sequence":"additional","affiliation":[{"name":"College of Food and Bioengineering, Bengbu University, Bengbu 233000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1016\/j.tplants.2023.12.014","article-title":"Plant organellar genomes: Much done, much more to do","volume":"29","author":"Wang","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"912","DOI":"10.1111\/tpj.15495","article-title":"Plant mitochondria\u2014Past, present and future","volume":"108","author":"Rasmusson","year":"2021","journal-title":"Plant J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1146\/annurev-arplant-043015-112232","article-title":"Plant mitochondrial genomes: Dynamics and mechanisms of mutation","volume":"68","author":"Gualberto","year":"2017","journal-title":"Annu. 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