{
  "abstract": "Plastomes are widely used in plant systematics and also retain signals of structural evolution. In this study, we investigated plastome evolution in the subfamily Aurantioideae of Rutaceae, focusing on structural variation at the LSC–IR boundary regions, putative pseudogenization of plastid genes, plastome-based classification of Citrus, and divergence-time patterns. Comparative analyses revealed substantial structural variation around the rpl22 and rps19 regions at the LSC–IR boundaries and repeated pseudogenization of plastid genes such as rpl22, ycf68, and orf56. Additional lineage-specific sequence disruptions were detected in cemA, ycf15, rps4, and ycf1. Phylogenetic analyses of complete plastomes from 56 Citrus accessions resolved eight major plastome clusters within Citrus. Divergence-time analysis indicated two comparable Asia–Africa splits within Aurantioideae, whereas the divergence between Australian and Asian Citrus lineages was more recent. These results show that plastome evolution in Aurantioideae combines phylogenetically informative sequence variation with recurrent local structural change and provides useful information for classification and evolutionary interpretation in this economically important plant group.",
  "abstract_shown": true,
  "affiliations": [
    "Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka",
    "Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan",
    "Graduate School of Advanced Health Science, Saga University, Saga, Japan",
    "The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan",
    "Faculty of Agriculture, Saga University, Saga, Japan",
    "Applied BioSciences, Macquarie University, Sydney, New South Wales, Australia"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Eranga Pawani Witharana"
    },
    {
      "affs": [
        1
      ],
      "name": "Myat Htoo San"
    },
    {
      "affs": [
        2
      ],
      "name": "Nadeeka U. Jayawardana"
    },
    {
      "affs": [
        3
      ],
      "name": "Nobuhiro Kotoda"
    },
    {
      "affs": [
        4
      ],
      "name": "Masashi Yamamoto"
    },
    {
      "affs": [
        5
      ],
      "name": "Yukio Nagano"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1ap9g4z3jbvy7.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0349882",
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  "id": "1ap9g4z3jbvy7",
  "issns": [
    "1932-6203"
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  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1105|Plant Diversity and Evolution"
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      "/Biology and life sciences/Plant science/Plant evolution/Plant phylogenetics"
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      "/Biology and life sciences/Taxonomy/Evolutionary systematics"
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    [
      "plos",
      "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis"
    ],
    [
      "plos",
      "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Plant phylogenetics"
    ],
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      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics"
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    [
      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics"
    ],
    [
      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis"
    ],
    [
      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Plant phylogenetics"
    ],
    [
      "plos",
      "/Earth sciences/Paleontology/Paleogenetics"
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      "plos",
      "/Ecology and environmental sciences/Conservation science/Conservation biology/Conservation genetics"
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      "plos",
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  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0349882&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-07",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/1ap9g4z3jbvy7.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:30Z",
      "native_id": "10.1371/journal.pone.0349882",
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      "url": "https://doi.org/10.1371/journal.pone.0349882"
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  "subjects": [
    {
      "field": "biology",
      "origin": "plos:evolutionary biology",
      "subfield": "evolutionary-biology"
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  ],
  "title": "Plastome evolution in Aurantioideae and plastome-based classification of Citrus",
  "title_text": "Plastome evolution in Aurantioideae and plastome-based classification of Citrus",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:30Z",
  "url": "https://research.draconitic.com/paper/1ap9g4z3jbvy7",
  "venue": "PLOS One",
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}