{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T17:59:12Z","timestamp":1791395952395,"version":"4.3.3"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["18K05623"],"award-info":[{"award-number":["18K05623"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    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\u2013IR boundary regions, putative pseudogenization of plastid genes, plastome-based classification of\n                    <jats:italic>Citrus<\/jats:italic>\n                    , and divergence-time patterns. Comparative analyses revealed substantial structural variation around the\n                    <jats:italic>rpl22<\/jats:italic>\n                    and\n                    <jats:italic>rps19<\/jats:italic>\n                    regions at the LSC\u2013IR boundaries and repeated pseudogenization of plastid genes such as\n                    <jats:italic>rpl22<\/jats:italic>\n                    ,\n                    <jats:italic>ycf68<\/jats:italic>\n                    , and\n                    <jats:italic>orf56<\/jats:italic>\n                    . Additional lineage-specific sequence disruptions were detected in\n                    <jats:italic>cemA<\/jats:italic>\n                    ,\n                    <jats:italic>ycf15<\/jats:italic>\n                    ,\n                    <jats:italic>rps4<\/jats:italic>\n                    , and\n                    <jats:italic>ycf1<\/jats:italic>\n                    . Phylogenetic analyses of complete plastomes from 56\n                    <jats:italic>Citrus<\/jats:italic>\n                    accessions resolved eight major plastome clusters within\n                    <jats:italic>Citrus<\/jats:italic>\n                    . Divergence-time analysis indicated two comparable Asia\u2013Africa splits within Aurantioideae, whereas the divergence between Australian and Asian\n                    <jats:italic>Citrus<\/jats:italic>\n                    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.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0349882","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T17:31:57Z","timestamp":1791394317000},"page":"e0349882","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plastome evolution in Aurantioideae and plastome-based classification of Citrus"],"prefix":"10.1371","volume":"21","author":[{"given":"Eranga Pawani","family":"Witharana","sequence":"first","affiliation":[{"name":"University of Peradeniya","place":["Peradeniya, Sri Lanka"],"department":["Faculty of Agriculture"]},{"name":"Saga University","place":["Saga, Japan"],"department":["Analytical Research Center for Experimental Sciences"]},{"name":"Saga University","place":["Saga, Japan"],"department":["Graduate School of Advanced Health Science"]},{"name":"Kagoshima University","place":["Kagoshima, Japan"],"department":["The United Graduate School of Agricultural Sciences"]},{"name":"Saga University","place":["Saga, Japan"],"department":["Faculty of Agriculture"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myat Htoo","family":"San","sequence":"additional","affiliation":[{"name":"Saga University","place":["Saga, Japan"],"department":["Analytical Research Center for Experimental Sciences"]},{"name":"Kagoshima University","place":["Kagoshima, Japan"],"department":["The United Graduate School of Agricultural Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadeeka U.","family":"Jayawardana","sequence":"additional","affiliation":[{"name":"University of Peradeniya","place":["Peradeniya, Sri Lanka"],"department":["Faculty of Agriculture"]},{"name":"Macquarie University","place":["Sydney, New South Wales, Australia"],"department":["Applied BioSciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nobuhiro","family":"Kotoda","sequence":"additional","affiliation":[{"name":"Saga University","place":["Saga, Japan"],"department":["Graduate School of Advanced Health Science"]},{"name":"Kagoshima University","place":["Kagoshima, Japan"],"department":["The United Graduate School of Agricultural Sciences"]},{"name":"Saga University","place":["Saga, Japan"],"department":["Faculty of Agriculture"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masashi","family":"Yamamoto","sequence":"additional","affiliation":[{"name":"Kagoshima University","place":["Kagoshima, Japan"],"department":["The United Graduate School of Agricultural Sciences"]},{"name":"Kagoshima University","place":["Kagoshima, Japan"],"department":["Faculty of 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