{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T08:25:02Z","timestamp":1787214302502,"version":"build-2736575974"},"reference-count":123,"publisher":"Pensoft Publishers","license":[{"start":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["imafungus"],"abstract":"<jats:p>\n                    The genus\n                    <jats:italic>Phytophthora (Oomycota)<\/jats:italic>\n                    comprises highly destructive and widely distributed plant pathogens that threaten global agriculture and forest ecosystems; however, the evolutionary significance of intraspecific and interspecific mitogenomic variation within this genus remains poorly understood. In this study, complete mitochondrial genomes of 11\n                    <jats:italic>Phytophthora<\/jats:italic>\n                    species, isolated from forest tree rhizospheres in the Qinling Mountains of China, were sequenced, assembled, and annotated to resolve their genetic diversity and evolutionary patterns. All 11 mitogenomes possess typical circular topologies, ranging in size from 37,502 bp (\n                    <jats:italic>P. citrophthora<\/jats:italic>\n                    ) to 41,542 bp (\n                    <jats:italic>P. cryptogea<\/jats:italic>\n                    ), with a uniform GC content averaging approximately 21.96%. The gene repertoire was highly conserved across all genomes, containing 34 core protein-coding genes (PCGs), two rRNA genes, 24\u201325 tRNA genes, and no introns. Selective pressure analysis showed that Ka\/Ks ratios for all 34 core PCGs were significantly below 1 (ranging from 0.0096 to 0.1737), demonstrating that purifying selection drives mitochondrial genome evolution in\n                    <jats:italic>Phytophthora<\/jats:italic>\n                    . Combined mitogenomic and multi-locus phylogenomics clarified the phylogenetic placement of these taxa and provided timescale estimates for their divergence. Overall, this work enriches the mitogenomic resources of\n                    <jats:italic>Phytophthora<\/jats:italic>\n                    from pristine natural ecosystems and establishes a critical genomic baseline for accurate species identification, taxonomic revisions, and the study of evolutionary dynamics in oomycetes.\n                  <\/jats:p>","DOI":"10.3897\/imafungus.17.203360","type":"journal-article","created":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T08:04:17Z","timestamp":1787213057000},"source":"Crossref","is-referenced-by-count":0,"title":["Mitochondrial genomic variation, evolutionary dynamics, and phylogeny of forest-associated Phytophthora species in the Qinling Mountains of China"],"prefix":"10.3897","volume":"17","author":[{"given":"Yijia","family":"Sun","sequence":"first","affiliation":[{"name":"The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi'an, China"},{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowei","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxin","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaling","family":"Li","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zengqiang","family":"Qian","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaokui","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"},{"name":"The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayaka","family":"Hieno","sequence":"additional","affiliation":[{"name":"Center for Environmental and Societal Sustainability, Gifu University, Gifu, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koji","family":"Kageyama","sequence":"additional","affiliation":[{"name":"Center for Environmental and Societal Sustainability, Gifu University, Gifu, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingzhu","family":"Li","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, Shaanxi Normal University, Xi'an, China"},{"name":"College of Life Sciences, Shaanxi Normal University, Xi'an, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2258","published-online":{"date-parts":[[2026,8,20]]},"reference":[{"key":"203360_B1","doi-asserted-by":"publisher","DOI":"10.3114\/sim.2023.106.05"},{"key":"203360_B2","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu028"},{"key":"203360_B3","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-026-12583-4"},{"key":"203360_B4","doi-asserted-by":"publisher","DOI":"10.1007\/s00294-005-0016-3"},{"key":"203360_B5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx198"},{"key":"203360_B6","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.2.573"},{"key":"203360_B7","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2012.08.023"},{"key":"203360_B8","doi-asserted-by":"publisher","DOI":"10.1007\/s10327-018-0822-3"},{"key":"203360_B9","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2007.10.010"},{"key":"203360_B10","doi-asserted-by":"publisher","DOI":"10.3390\/jof8030303"},{"key":"203360_B11","doi-asserted-by":"publisher","DOI":"10.1186\/s43008-022-00097-z"},{"key":"203360_B12","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens14010103"},{"key":"203360_B13","doi-asserted-by":"publisher","DOI":"10.1111\/ecog.03904"},{"key":"203360_B14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0231296"},{"key":"203360_B15","unstructured":"Cao XR, Zhu XQ, Guo LY (2017) Three Chinese new records of Phytophthora isolated from Beijing water system. Mycosystema 36: 1664\u20131672."},{"key":"203360_B16","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw074"},{"key":"203360_B17","doi-asserted-by":"publisher","DOI":"10.3114\/sim.2022.101.06"},{"key":"203360_B18","doi-asserted-by":"publisher","DOI":"10.1111\/mpp.13345"},{"key":"203360_B19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv784"},{"key":"203360_B20","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12398"},{"key":"203360_B21","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.13269"},{"key":"203360_B22","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2289704"},{"key":"203360_B23","unstructured":"De Bary A (1876) Researches into the nature of the potato fungus Phytophthora infestans. Journal of the Royal Agricultural Society of England Series 2 12: 239\u2013269."},{"key":"203360_B24","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaf209"},{"key":"203360_B25","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-6365-y"},{"key":"203360_B26","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2015.08.011"},{"key":"203360_B27","doi-asserted-by":"publisher","DOI":"10.2307\/3761286"},{"key":"203360_B28","doi-asserted-by":"publisher","DOI":"10.1002\/1873-3468.13995"},{"key":"203360_B29","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00765"},{"key":"203360_B30","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.118.301237"},{"key":"203360_B31","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.12153"},{"key":"203360_B32","doi-asserted-by":"publisher","DOI":"10.1080\/15572536.2005.11832898"},{"key":"203360_B33","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz238"},{"key":"203360_B34","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syq010"},{"key":"203360_B35","doi-asserted-by":"publisher","DOI":"10.3852\/07-203"},{"key":"203360_B36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-57955-8"},{"key":"203360_B37","doi-asserted-by":"publisher","DOI":"10.5962\/p.415993"},{"key":"203360_B38","doi-asserted-by":"publisher","DOI":"10.1042\/bcj20190767"},{"key":"203360_B39","doi-asserted-by":"publisher","DOI":"10.3852\/10-058"},{"key":"203360_B40","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.14022"},{"key":"203360_B41","doi-asserted-by":"publisher","DOI":"10.1111\/efp.12015"},{"key":"203360_B42","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgeb.2025.100629"},{"key":"203360_B43","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02154-5"},{"key":"203360_B44","doi-asserted-by":"publisher","DOI":"10.3767\/003158509x442612"},{"key":"203360_B45","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0329.1996.tb00846.x"},{"key":"203360_B46","doi-asserted-by":"publisher","DOI":"10.1017\/S0953756298007734"},{"key":"203360_B47","doi-asserted-by":"publisher","DOI":"10.1111\/ppa.12564"},{"key":"203360_B48","doi-asserted-by":"publisher","DOI":"10.3767\/persoonia.2018.40.08"},{"key":"203360_B49","doi-asserted-by":"publisher","DOI":"10.3390\/f11010093"},{"key":"203360_B50","doi-asserted-by":"publisher","DOI":"10.3390\/jof7030226"},{"key":"203360_B51","doi-asserted-by":"publisher","DOI":"10.3767\/persoonia.2022.49.01"},{"key":"203360_B52","doi-asserted-by":"publisher","DOI":"10.3114\/sim.2024.107.04"},{"key":"203360_B53","doi-asserted-by":"publisher","DOI":"10.1007\/s10327-002-0037-4"},{"key":"203360_B54","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"203360_B55","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw268"},{"key":"203360_B56","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-025-02115-z"},{"key":"203360_B57","doi-asserted-by":"publisher","DOI":"10.3852\/10-278"},{"key":"203360_B58","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2004.03.007"},{"key":"203360_B59","doi-asserted-by":"publisher","DOI":"10.1079\/9781780640938.0000"},{"key":"203360_B60","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evz181"},{"key":"203360_B61","doi-asserted-by":"publisher","DOI":"10.1017\/S0953756204001431"},{"key":"203360_B62","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-7-r73"},{"key":"203360_B63","unstructured":"Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997."},{"key":"203360_B64","doi-asserted-by":"publisher","DOI":"10.1094\/PDIS-01-11-0076"},{"key":"203360_B65","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.002254"},{"key":"203360_B66","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.71105"},{"key":"203360_B67","doi-asserted-by":"publisher","DOI":"10.3390\/ijms252011186"},{"key":"203360_B68","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.2007.00114.x"},{"key":"203360_B69","doi-asserted-by":"crossref","unstructured":"Liu Z, Yang Y, Wang X et al. (2025) Pathogenic diversity and fungicide sensitivity of soybean root rot oomycetes in Heilongjiang Province, China. Pest Management Science 81: 8881.","DOI":"10.1002\/ps.8881"},{"key":"203360_B70","doi-asserted-by":"publisher","DOI":"10.3390\/d15090951"},{"key":"203360_B71","doi-asserted-by":"publisher","DOI":"10.3390\/agronomy14122810"},{"key":"203360_B72","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evt181"},{"key":"203360_B73","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.806398"},{"key":"203360_B74","unstructured":"Martin FN, Richardson P (2007) Mitochondrial genomics in the genus Phytophthora with a focus on Phytophthora ramorum. In: Proceedings of the Sudden Oak Death Third Science Symposium, Santa Rosa, CA."},{"key":"203360_B75","doi-asserted-by":"publisher","DOI":"10.1080\/15572536.2004.11833112"},{"key":"203360_B76","doi-asserted-by":"publisher","DOI":"10.1007\/s00294-007-0121-6"},{"key":"203360_B77","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2014.02.006"},{"key":"203360_B78","doi-asserted-by":"publisher","DOI":"10.1101\/411470"},{"key":"203360_B79","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-14-101"},{"key":"203360_B80","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2670"},{"key":"203360_B81","doi-asserted-by":"publisher","DOI":"10.1093\/nsr\/nwab032"},{"key":"203360_B82","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"203360_B83","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-09512-2"},{"key":"203360_B84","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.41.110306.130119"},{"key":"203360_B85","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010822"},{"key":"203360_B86","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"203360_B87","doi-asserted-by":"publisher","DOI":"10.1111\/jeu.12092"},{"key":"203360_B88","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv566"},{"key":"203360_B89","doi-asserted-by":"publisher","DOI":"10.1007\/s002940050220"},{"key":"203360_B90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0165072"},{"key":"203360_B91","doi-asserted-by":"publisher","DOI":"10.3390\/ani16020279"},{"key":"203360_B92","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-34059-1"},{"key":"203360_B93","doi-asserted-by":"publisher","DOI":"10.1080\/15572536.2003.11833177"},{"key":"203360_B94","doi-asserted-by":"publisher","DOI":"10.1111\/j.1755-0998.2011.03041.x"},{"key":"203360_B95","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.3.3.159"},{"key":"203360_B96","doi-asserted-by":"publisher","DOI":"10.1007\/s11557-015-1129-9"},{"key":"203360_B97","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-018-9350-5"},{"key":"203360_B98","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0143234"},{"key":"203360_B99","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2006.03.003"},{"key":"203360_B100","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-3059.2007.01689.x"},{"key":"203360_B101","doi-asserted-by":"publisher","DOI":"10.3767\/003158509x415450"},{"key":"203360_B102","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2022.107654"},{"key":"203360_B103","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2015.08.036"},{"key":"203360_B104","doi-asserted-by":"publisher","DOI":"10.1007\/s00122-002-1031-0"},{"key":"203360_B105","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2017.05.007"},{"key":"203360_B106","doi-asserted-by":"publisher","DOI":"10.1186\/s43008-021-00068-w"},{"key":"203360_B107","doi-asserted-by":"publisher","DOI":"10.1016\/j.funbio.2010.12.013"},{"key":"203360_B108","doi-asserted-by":"publisher","DOI":"10.3852\/mycologia.98.3.410"},{"key":"203360_B109","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963"},{"key":"203360_B110","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac049"},{"key":"203360_B111","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2011.12.002"},{"key":"203360_B112","doi-asserted-by":"publisher","DOI":"10.3390\/f10100927"},{"key":"203360_B113","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02334"},{"key":"203360_B114","doi-asserted-by":"publisher","DOI":"10.5598\/imafungus.2017.08.02.09"},{"key":"203360_B115","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm088"},{"key":"203360_B116","doi-asserted-by":"publisher","DOI":"10.3390\/d14070538"},{"key":"203360_B117","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01484"},{"key":"203360_B118","doi-asserted-by":"publisher","DOI":"10.1111\/j.1439-0434.2008.01441.x"},{"key":"203360_B119","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13096"},{"key":"203360_B120","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2021.12.002"},{"key":"203360_B121","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.70095"},{"key":"203360_B122","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.988368"},{"key":"203360_B123","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-022-08607-4"}],"container-title":["IMA Fungus"],"original-title":[],"link":[{"URL":"https:\/\/imafungus.pensoft.net\/article\/203360\/download\/pdf\/","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/imafungus.pensoft.net\/article\/203360\/download\/xml\/","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/imafungus.pensoft.net\/article_preview.php?id=203360&skip_redirect=1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T08:04:29Z","timestamp":1787213069000},"score":1,"resource":{"primary":{"URL":"https:\/\/imafungus.pensoft.net\/article\/203360\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,20]]},"references-count":123,"URL":"https:\/\/doi.org\/10.3897\/imafungus.17.203360","relation":{},"ISSN":["2210-6359","2210-6340"],"issn-type":[{"value":"2210-6359","type":"electronic"},{"value":"2210-6340","type":"print"}],"subject":[],"published":{"date-parts":[[2026,8,20]]},"article-number":"e203360"}}