{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T10:50:36Z","timestamp":1791283836223,"version":"4.1.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:00:00Z","timestamp":1784592000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:00:00Z","timestamp":1784592000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"The Science and Technology Research Program of Chongqing Municipal Education Commission","award":["No. KJQN202515101"],"award-info":[{"award-number":["No. KJQN202515101"]}],"id":[{"id":"https:\/\/ror.org\/031nm5713","id-type":"ROR","asserted-by":"crossref"}]},{"name":"The Fundamental Scientific Research Funds Project of Chongqing Municipal Science and Technology Bureau","award":["No. CSTB2025jxjl-jbkyX0017"],"award-info":[{"award-number":["No. CSTB2025jxjl-jbkyX0017"]}],"id":[{"id":"https:\/\/ror.org\/03ze5ke63","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. U25A20162"],"award-info":[{"award-number":["No. U25A20162"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019071","name":"Chongqing Science and Technology Innovation Leading Talent Support Program","doi-asserted-by":"publisher","award":["No. CQYC20220301627"],"award-info":[{"award-number":["No. CQYC20220301627"]}],"id":[{"id":"10.13039\/501100019071","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Microbiol"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1007\/s00203-026-05044-9","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T08:41:28Z","timestamp":1784623288000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative mitochondrial genomics of Ophiocordycipitaceae fungi reveals AT bias and site-specific positive selection in the nad4 gene"],"prefix":"10.1007","volume":"208","author":[{"given":"Qiuyang","family":"Wei","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanchuan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijiang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,21]]},"reference":[{"key":"5044_CR1","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/S1055-7903(03)00194-5","volume":"29","author":"KL Adams","year":"2003","unstructured":"Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380\u2013395. https:\/\/doi.org\/10.1016\/S1055-7903(03)00194-5","journal-title":"Mol Phylogenet Evol"},{"key":"5044_CR2","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1093\/gbe\/evu028","volume":"6","author":"G Aguileta","year":"2014","unstructured":"Aguileta G, de Vienne DM, Ross ON, Hood ME, Giraud T, Petit E (2014) High variability of mitochondrial gene order among fungi. Genome Biol Evol 6:451\u2013465. https:\/\/doi.org\/10.1093\/gbe\/evu028","journal-title":"Genome Biol Evol"},{"key":"5044_CR3","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1093\/oxfordjournals.molbev.a003945","volume":"18","author":"M Anisimova","year":"2001","unstructured":"Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18:1585\u20131592. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a003945","journal-title":"Mol Biol Evol"},{"issue":"10","key":"5044_CR4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3003433","volume":"23","author":"T Badet","year":"2025","unstructured":"Badet T, Croll D (2025) Phylogenomic signatures of repeat-induced point mutations across the fungal kingdom. PLoS Biol 23(10):e3003433. https:\/\/doi.org\/10.1371\/journal.pbio.3003433","journal-title":"PLoS Biol"},{"key":"5044_CR5","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s12915-024-01824-1","volume":"22","author":"A Butenko","year":"2024","unstructured":"Butenko A, Luke\u0161 J, Speijer D, Wideman JG (2024) Mitochondrial genomes revisited: why do different lineages retain different genes? BMC Biol 22:15\u201331. https:\/\/doi.org\/10.1186\/s12915-024-01824-1","journal-title":"BMC Biol"},{"key":"5044_CR6","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422\u20131423. https:\/\/doi.org\/10.1093\/bioinformatics\/btp163","journal-title":"Bioinformatics"},{"key":"5044_CR7","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/S0921-8777(99)00025-7","volume":"434","author":"DL Croteau","year":"1999","unstructured":"Croteau DL, Stierum RH, Bohr VA (1999) Mitochondrial DNA repair pathways. Mutat Res 434:137\u2013148. https:\/\/doi.org\/10.1016\/S0921-8777(99)00025-7","journal-title":"Mutat Res"},{"key":"5044_CR8","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.fgb.2013.01.009","volume":"55","author":"C Ferandon","year":"2013","unstructured":"Ferandon C, Xu J, Barroso G (2013) The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences. Fungal Genet Biol 55:85\u201391. https:\/\/doi.org\/10.1016\/j.fgb.2013.01.009","journal-title":"Fungal Genet Biol"},{"key":"5044_CR9","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/sysbio\/syq010","volume":"59","author":"S Guindon","year":"2010","unstructured":"Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307\u2013321. https:\/\/doi.org\/10.1093\/sysbio\/syq010","journal-title":"Syst Biol"},{"key":"5044_CR10","doi-asserted-by":"publisher","DOI":"10.3390\/jof11120892","volume":"11","author":"Z He","year":"2025","unstructured":"He Z, Ye M, Wu H, Liang D, Huan J, Yao Y, Wu X, Luo X (2025) The conservation crisis of Ophiocordyceps sinensis: strategies, challenges, and sustainable future of artificial cultivation. J Fungi 11:892. https:\/\/doi.org\/10.3390\/jof11120892","journal-title":"J Fungi"},{"key":"5044_CR11","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1146\/annurev-biochem-070511-103700","volume":"82","author":"J Hirst","year":"2013","unstructured":"Hirst J (2013) Mitochondrial complex I. Annu Rev Biochem 82:551\u2013575. https:\/\/doi.org\/10.1146\/annurev-biochem-070511-103700","journal-title":"Annu Rev Biochem"},{"key":"5044_CR12","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","volume":"35","author":"DT Hoang","year":"2018","unstructured":"Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518\u2013522. https:\/\/doi.org\/10.1093\/molbev\/msx281","journal-title":"Mol Biol Evol"},{"key":"5044_CR13","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1605218","volume":"16","author":"J Jia","year":"2025","unstructured":"Jia J, Li C, Tang M, Liao H, Yang Z, Wang Y, Li M, Zeng W, Wang Y (2025) Mitochondrial genome characterization, evolution and intron dynamics of the entomopathogenic genus Cordyceps. Front Microbiol 16:1605218. https:\/\/doi.org\/10.3389\/fmicb.2025.1605218","journal-title":"Front Microbiol"},{"key":"5044_CR14","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-698","volume":"13","author":"V Joardar","year":"2012","unstructured":"Joardar V, Abrams NF, Hostetler J, Paukstelis PJ, Pakala S, Pakala SB et al (2012) Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. BMC Genomics 13:698. https:\/\/doi.org\/10.1186\/1471-2164-13-698","journal-title":"BMC Genomics"},{"key":"5044_CR15","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","volume":"14","author":"S Kalyaanamoorthy","year":"2017","unstructured":"Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) Modelfinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587\u2013589. https:\/\/doi.org\/10.1038\/nmeth.4285","journal-title":"Nat Methods"},{"key":"5044_CR16","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/emboj.2012.300","volume":"32","author":"WJH Koopman","year":"2013","unstructured":"Koopman WJH, Distelmaier F, Smeitink JAM, Willems PHGM (2013) OXPHOS mutations and neurodegeneration. EMBO J 32:9\u201329. https:\/\/doi.org\/10.1038\/emboj.2012.300","journal-title":"EMBO J"},{"key":"5044_CR17","doi-asserted-by":"publisher","first-page":"16246","DOI":"10.1038\/srep16246","volume":"5","author":"Y Li","year":"2015","unstructured":"Li Y, Hu XD, Yang RH, Hsiang T, Wang K, Liang DQ et al (2015) Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis. Sci Rep 5:16246. https:\/\/doi.org\/10.1038\/srep16246","journal-title":"Sci Rep"},{"key":"5044_CR18","doi-asserted-by":"publisher","first-page":"1727","DOI":"10.1126\/science.1118884","volume":"311","author":"M Lynch","year":"2006","unstructured":"Lynch M, Koskella B, Schaack S (2006) Mutation pressure and the evolution of organelle genomic architecture. Science 311:1727\u20131730. https:\/\/doi.org\/10.1126\/science.1118884","journal-title":"Science"},{"key":"5044_CR19","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530\u20131534. https:\/\/doi.org\/10.1093\/molbev\/msaa015","journal-title":"Mol Biol Evol"},{"key":"5044_CR20","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1093\/oxfordjournals.molbev.a040410","volume":"3","author":"M Nei","year":"1986","unstructured":"Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418\u2013426. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a040410","journal-title":"Mol Biol Evol"},{"key":"5044_CR21","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1007\/s00294-014-0439-9","volume":"61","author":"A Ortiz-Urquiza","year":"2015","unstructured":"Ortiz-Urquiza A, Keyhani NO (2015) Stress response signaling and virulence: insights from entomopathogenic fungi. Curr Genet 61:239\u2013249. https:\/\/doi.org\/10.1007\/s00294-014-0439-9","journal-title":"Curr Genet"},{"issue":"1","key":"5044_CR22","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1038\/nrg2899","volume":"12","author":"JB Plotkin","year":"2011","unstructured":"Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12(1):32\u201342. https:\/\/doi.org\/10.1038\/nrg2899","journal-title":"Nat Rev Genet"},{"key":"5044_CR23","doi-asserted-by":"publisher","first-page":"121","DOI":"10.5598\/imafungus.2014.05.01.12","volume":"5","author":"CA Quandt","year":"2014","unstructured":"Quandt CA, Kepler RM, Gams W, Araujo JPM, Ban S, Evans HC et al (2014) Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus 5:121\u2013134. https:\/\/doi.org\/10.5598\/imafungus.2014.05.01.12","journal-title":"IMA Fungus"},{"key":"5044_CR24","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406\u2013425","journal-title":"Mol Biol Evol"},{"key":"5044_CR25","doi-asserted-by":"publisher","first-page":"9433","DOI":"10.1007\/s00253-018-9350-5","volume":"102","author":"S Sandor","year":"2018","unstructured":"Sandor S, Zhang Y, Xu J (2018) Fungal mitochondrial genomes and genetic polymorphisms. Appl Microbiol Biotechnol 102:9433\u20139448. https:\/\/doi.org\/10.1007\/s00253-018-9350-5","journal-title":"Appl Microbiol Biotechnol"},{"key":"5044_CR26","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","volume":"15","author":"PM Sharp","year":"1987","unstructured":"Sharp PM, Li WH (1987) The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281\u20131295. https:\/\/doi.org\/10.1093\/nar\/15.3.1281","journal-title":"Nucleic Acids Res"},{"key":"5044_CR27","doi-asserted-by":"publisher","first-page":"1182","DOI":"10.1126\/science.322.5905.1182","volume":"322","author":"R Stone","year":"2008","unstructured":"Stone R (2008) Mycology: last stand for the body snatcher of the Himalayas? Science 322:1182. https:\/\/doi.org\/10.1126\/science.322.5905.1182","journal-title":"Science"},{"key":"5044_CR28","doi-asserted-by":"publisher","first-page":"5","DOI":"10.3114\/sim.2007.57.01","volume":"57","author":"GH Sung","year":"2007","unstructured":"Sung GH, Hywel-Jones NL, Sung JM, Luangsa-ard JJ, Shrestha B, Spatafora JW (2007) Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud Mycol 57:5\u201359. https:\/\/doi.org\/10.3114\/sim.2007.57.01","journal-title":"Stud Mycol"},{"key":"5044_CR29","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nrg1271","volume":"5","author":"JN Timmis","year":"2004","unstructured":"Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123\u2013135. https:\/\/doi.org\/10.1038\/nrg1271","journal-title":"Nat Rev Genet"},{"key":"5044_CR30","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/0378-1119(90)90491-9","volume":"87","author":"F Wright","year":"1990","unstructured":"Wright F (1990) The effective number of codons used in a gene. Gene 87:23\u201329","journal-title":"Gene"},{"key":"5044_CR31","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","volume":"155","author":"Z Yang","year":"2000","unstructured":"Yang Z, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431\u2013449. https:\/\/doi.org\/10.1093\/genetics\/155.1.431","journal-title":"Genetics"},{"key":"5044_CR32","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1093\/molbev\/msi097","volume":"22","author":"Z Yang","year":"2005","unstructured":"Yang Z, Wong WSW, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107\u20131118. https:\/\/doi.org\/10.1093\/molbev\/msi097","journal-title":"Mol Biol Evol"},{"key":"5044_CR33","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586\u20131591. https:\/\/doi.org\/10.1093\/molbev\/msm088","journal-title":"Mol Biol Evol"}],"container-title":["Archives of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-05044-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-026-05044-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-026-05044-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T09:53:01Z","timestamp":1791280381000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00203-026-05044-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,21]]},"references-count":33,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["5044"],"URL":"https:\/\/doi.org\/10.1007\/s00203-026-05044-9","relation":{},"ISSN":["0302-8933","1432-072X"],"issn-type":[{"value":"0302-8933","type":"print"},{"value":"1432-072X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,21]]},"assertion":[{"value":"30 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 June 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 June 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"502"}}