{
  "abstract": "Background/objectives\n\nActinidia rufa provides a wild kiwifruit resource for examining mitochondrial sequence conservation and structural variation. We examined the hypothesis that coding-sequence (CDS) coordinates retain higher interspecific alignment coverage than non-CDS coordinates despite differences in block organization. We also assessed reference support, repeat-associated junctions, and mitochondrial gene-tree concordance.Methods\n\nNC_086781.1 was evaluated using PacBio HiFi reads (CRR3429456), uniform repeat-junction screening, six interspecific one-to-one comparisons, repeat and mitochondrial plastid DNA (MTPT) masking, and single-gene trees.Results\n\nThe 1,022,459 bp reference contains 39 protein-coding loci. Across six comparisons, CDS coverage was 99.90-100%, versus 68.94-87.79% for non-CDS sequence; adjusted circular-shift p values were 0.001674-0.008745. Homologous sequence occurred in 32-61 merged blocks per comparison, and separate repeat and MTPT masks retained 94.39-98.29% and 93.60-99.39% of baseline aligned reference sequence, respectively. Stringent competitive mapping gave a mean depth of 40.35× and breadth of 73.9% at ≥1×. Of 192 repeat pairs ≥50 bp, 41 were evaluable and none met the reciprocal-alternative-support rule; R43 and R47 each had one-sided single-read support. Eight of 16 informative gene trees contained the A. rufa-A. chinensis split, but phylogenetic information was limited.Conclusions\n\nThe comparisons support higher CDS than non-CDS coordinate coverage within a reference set with variable block organization. Repeat-junction support and single-gene resolution remain limited; the data do not establish ongoing recombination, an exclusive circular physical architecture, or a mitochondrial contribution to waterlogging tolerance.",
  "abstract_shown": true,
  "affiliations": [
    "College of Food and Bioengineering, Bengbu University, Bengbu 233000, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Chengcheng Ling"
    },
    {
      "affs": [
        0
      ],
      "name": "Zirou Xie"
    },
    {
      "affs": [
        0
      ],
      "name": "Hang Yuan"
    },
    {
      "affs": [
        0
      ],
      "name": "Jun Yang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e79hrgv9rky6c.bib",
  "cited_by": 0,
  "doi": "10.3390/genes17101209",
  "fulltext_url": "https://europepmc.org/articles/PMC13704310",
  "id": "e79hrgv9rky6c",
  "issns": [
    "2073-4425"
  ],
  "landing_url": "https://europepmc.org/article/MED/42938325",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7214734611",
  "pdf_url": "https://europepmc.org/articles/PMC13704310?pdf=render",
  "pmcid": "PMC13704310",
  "pmid": "42938325",
  "published": "2026-09-29",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/e79hrgv9rky6c.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:24Z",
      "native_id": "MED:42938325",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42938325"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Characterization and Comparative Analysis of the Actinidia rufa Mitochondrial Genome.",
  "title_text": "Characterization and Comparative Analysis of the Actinidia rufa Mitochondrial Genome.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:22:24Z",
  "url": "https://research.draconitic.com/paper/e79hrgv9rky6c",
  "venue": "Genes",
  "versions": []
}