Complete Genome Sequence of Candida mucifera from an Otitis Media Patient

Complete Genome Sequence of Candida mucifera from an Otitis Media Patient | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Complete Genome Sequence of Candida mucifera from an Otitis Media Patient Rongchen Dai, Jing Guan, Yating Ning, Timothy Kudinha, Wei Zhang, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4134268/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Sep, 2024 Read the published version in Mycopathologia → Version 1 posted 6 You are reading this latest preprint version Abstract We describe for the first time, a high-quality genome for a rare human yeast pathogen Candida mucifera , from a patient with chronic suppurative otitis media. Antifungal susceptibility profile was determined, and a potential mechanism responsible for intrinsically reduced azole susceptibility in Trichomonascus ciferrii-Candida mucifera species complex was proposed. Candida mucifera Fungal infection Whole genome sequencing Reduced azole susceptibility Resistant mechanism Full Text The yeast species Candida mucifera (also referred to as Blastobotrys mucifer in a recent study [1]) falls within the Trichomonascus ciferrii species complex as per the latest NCBI taxonomy database (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=191334). This species complex is composed of ascomycetous heterothallic yeasts, formerly referred to as the Stephanoascus ciferrii complex, and currently comprises three species, namely Trichomonascus ciferrii , Candida allociferrii , and C. mucifera [2]. C. mucifera is a rare human fungal pathogen, which has only been reported in China in chronic suppurative otitis media cases [3]. Additionally, this species has been detected in environmental and animal sources (https://wi.knaw.nl/page/fungal_display/3954) [4]. Of note, all previously described animal and clinical strains exhibited notable reduced fluconazole susceptibility with minimal inhibitory concentration [MIC] values ranging from 32 to 128 mg/L) [3]. The isolate described in this study originated from an 8-year-old boy admitted to a hospital in South China (2018), suffering from chronic suppurative otitis media and repeated otorrhea (with yellow abscess) for two years. He had a moderate hearing loss but with no significant symptoms of pain, fever, or bleeding in ears. Specialized examination revealed large perforations in both eardrums, and hence tympanoplasty was carried out. Intraoperative tissue was sent for routine culture in the local mycology lab, and yeast colonies (isolate ID no. 17G1312) were observed which were initially identified as “ T. ciferrii ” by VITEK 2 Yeast Identification Card (bioMérieux, France). On Sabouraud dextrose medium (Thermo, USA), the isolate exhibited pale yellow yeast colonies after incubation at 35°C for 72 hours. When cultured on Candida chromogenic medium (CHROMagar, France), the colonies appeared blue to green in color (Supplementary Figure 1). Antifungal susceptibility testing was performed on the isolate using YeastOne Sensititre (Thermo, USA). After 48 hours of incubation, the MICs of the tested isolate were as follows: fluconazole 16 mg/L, itraconazole 0.25 mg/L, voriconazole 0.12 mg/L, posaconazole 0.25 mg/L, micafungin 0.03 mg/L, anidulafungin 0.03 mg/L, caspofungin 0.03 mg/L, flucytosine 0.5 mg/L, and amphotericin B 1 mg/L. The internal transcribed spacer (ITS) region of isolate 17G1312 was amplified and sequenced using ABI 3730xl platform (Thermo, USA). The strain’s sequence was 100% (576/576) identical to that of C. mucifera strain 80408 (GenBank accession no. OR761613.1) and 99.5% (555/558) to C. mucifera type strain CBS 7409 T (GenBank accession no. NR_130678.1), but only 95.4% (554/581) similarity to T. ciferrii type strain CBS 5295 T (GenBank accession no. NR_111160.1). The maximum likelihood tree constructed based on ITS region sequences, further support assigning the isolate 17G1312 as C. mucifera (Supplementary Figure 2). As there was no publicly available genome information for C. mucifera , we conducted whole-genome sequencing of the isolate 17G1312 using short-reads on the Illumina MiSeq PE150 (Illumina, USA) and long-reads on the PacBio Sequel II (PacBio, USA). The assembly process involved converting the BAM file to a FASTA file using SAMtools v1.9 [5], assembly using Flye v2.9.3 [6], and polishing the assembly results using Pilon v1.23, with short reads filtered by fastp v0.23.4 [7, 8]. The genome completeness was assessed using BUSCO v5.2.2 and the saccharomycetes_odb10 database [9], revealing an integrity of 96.2% (single-copy: 95.5%, duplicated: 0.7%). The genome of this new strain comprises 8 scaffolds with a total length of 16,402,853 bp (15.6 Mb). The N50 is 2,475,350 bp, and the GC content is 44.9%. The genome of isolate 17G1312 (GenBank assembly accession: GCA_036871495.1) was compared with two genomes of its closely-related species T. ciferrii (strains NRRL Y-10943 [GenBank assembly accession: GCA_030573635.1], and CBS 4856 [GenBank assembly accession: GCA_008704605.1]) using fastANI v1.33 [10], and the average nucleotide identity (ANI) between isolate 17G1312 and two T. ciferrii strains, was only 80.6%. Gene annotation results of T. ciferrii strain CBS 4856 were used to train a new de novo prediction model for AUGUSTUS v3.3.2 and then utilized for structural annotation of our C. mucifera genome [11], and a total of 6533 genes were predicted. Due to the “intrinsically” reduced fluconazole susceptibility in C. mucifera and other species of the T. ciferrii complex [3], we conducted an mutation analysis of the azole target Erg11p. We observed that position 499 of Erg11p amino acid sequence in C. mucifera isolate 17G1312 (GenBank accession no. PP204302.1), and the homologous position (position 501) in T. ciferrii (GenBank accession no. PP213130.1), had a valine (V) residue. In contrast to this finding, in wild-type azole-susceptible Candida albicans strains (e.g. strain no. SC5314, GenBank accession no. XP_716761.1), the homologous position of Erg11p at position 488 has an isoleucine (I) residue. Of note, the V488I amino acid substitution in C. albicans has been reported to be responsible for fluconazole resistance [12]. Consequently, we hypothesize that the V499I substitution in C. mucifera Erg11p (corresponding to V501I substitution in T. ciferrii ) introduced reduced fluconazole susceptibility within this species complex. In summary, we described (and deposited) the complete genome of a rare human yeast pathogen, C. mucifera . In addition, our analysis provides a potential mechanism explanation for “intrinsically” reduced azole susceptibility in Trichomonascus ciferrii-Candida mucifera species complex. The methodology used, as well as the availability of data and stock cultures, adheres to the quality assurance checklist of MycopathologiaGENOMES [13]. Declarations Data availability The isolate 17G1312 has been deposited at China General Microbiological Culture Collection Center under the accession number CGMCC2.8257. The ERG11 , ITS, D1/D2 region of the isolate 17G1312 have been released in GenBank (accession nos. PP204302.1, PP204071.1, PP230918.1). All sequencing data have been deposited in the NCBI database (GenBank accession nos. CP145483.1-CP145490.1, assembly accession no. GCA_036871495.1, Biosample no. SAMN39602682, BioProject no. PRJNA1068766). Funding This work was financially supported by the National Key Research and Development Program of China (2022YFC2303002), and the National High Level Hospital Clinical Research Funding (2022-PUMCH-C-052). Author Contributions M. X. and Y.-C. X. conceived and planned the experiments. R.-C. D. and M. X. performed the genomic analysis. J. G., Y.-T. N., W. Z., X.-F. C. and G. Z. collected the isolate and clinical data. R.-C. D., Y.-T. N. and M. X. contributed to the first draft of the manuscript. J. G., T. K., and Y.-C. X. contributed to the review and editing. Ethics approval This study was approved by the Human Research Ethics Committee of Peking Union Medical College Hospital (No. S-263). Conflict of interest The authors have no relevant financial or non-financial interests to disclose. References Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast. 2023;40(1):7-31. Ueda-Nishimura K, Mikata K. Species distinction of the ascomycetous heterothallic yeast-like fungus Stephanoascus ciferrii complex: description of Candida allociferrii sp. nov. and reinstatement of Candida mucifera Kockova-Kratochvilova et Slavikova. Int J Syst Evol Microbiol. 2002;52(Pt 2):463-71. Guo P, Wu Z, Liu P, Chen Y, Liao K, Peng Y, et al. Identification and Antifungal Susceptibility Analysis of Stephanoascus ciferrii Complex Species Isolated From Patients With Chronic Suppurative Otitis Media. Front Microbiol. 2021;12:680060. Shoubao Y, Jie Y, TingTing S, Jiaquan G, Cuie S. Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor. AMB Express. 2023;13(1):56. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. BIOINFORMATICS. 2009;25(16):2078-9. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540-6. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i90. Manni M, Berkeley MR, Seppey M, Simao FA, Zdobnov EM. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38(10):4647-54. Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008;24(5):637-44. Manastir L, Ergon MC, Yucesoy M. Investigation of mutations in Erg11 gene of fluconazole resistant Candida albicans isolates from Turkish hospitals. Mycoses. 2011;54(2):99-104. Mac Aogain M, Chaturvedi V, Chotirmall SH. MycopathologiaGENOMES: The New 'Home' for the Publication of Fungal Genomes. Mycopathologia. 2019;184(5):551-4. Supplementary Files SupplementaryData.docx Cite Share Download PDF Status: Published Journal Publication published 02 Sep, 2024 Read the published version in Mycopathologia → Version 1 posted Editorial decision: Minor revisions 17 Jun, 2024 Reviewers agreed at journal 28 May, 2024 Reviewers invited by journal 24 Apr, 2024 Editor invited by journal 02 Apr, 2024 Editor assigned by journal 01 Apr, 2024 First submitted to journal 31 Mar, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4134268","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":294942865,"identity":"69fed3d5-f881-4aec-a527-2b491e48f685","order_by":0,"name":"Rongchen 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\u003cem\u003eBlastobotrys mucifer\u0026nbsp;\u003c/em\u003ein a recent study\u0026nbsp;[1]) falls within the \u003cem\u003eTrichomonascus ciferrii\u003c/em\u003e species complex as per the latest NCBI taxonomy database (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=191334). This species complex is composed of ascomycetous heterothallic yeasts, formerly referred to as the \u003cem\u003eStephanoascus ciferrii\u003c/em\u003e complex, and currently comprises three species, namely \u003cem\u003eTrichomonascus ciferrii\u003c/em\u003e, \u003cem\u003eCandida allociferrii\u003c/em\u003e, and \u003cem\u003eC. mucifera\u003c/em\u003e [2]. \u003cem\u003eC. mucifera\u003c/em\u003e is a rare human fungal pathogen, which has only been reported in China in chronic suppurative otitis media cases\u0026nbsp;[3]. Additionally, this species has been detected in environmental and animal sources (https://wi.knaw.nl/page/fungal_display/3954)\u0026nbsp;[4]. Of note, all previously described animal and clinical strains exhibited notable reduced fluconazole susceptibility with minimal inhibitory concentration [MIC] values ranging from 32 to 128 mg/L)\u0026nbsp;[3].\u003c/p\u003e\n\u003cp\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;The isolate described in this study originated from an 8-year-old boy admitted to a hospital in South China (2018), suffering from chronic suppurative otitis media and repeated otorrhea (with yellow abscess) for two years. He had a moderate hearing loss but with no significant symptoms of pain, fever, or bleeding in ears. Specialized examination revealed large perforations in both eardrums, and hence tympanoplasty was carried out. Intraoperative tissue was sent for routine culture in the local mycology lab, and yeast colonies (isolate ID no. 17G1312) were observed which were initially identified as \u0026ldquo;\u003cem\u003eT. ciferrii\u003c/em\u003e\u0026rdquo; by VITEK 2 Yeast Identification Card (bioM\u0026eacute;rieux, France).\u003c/p\u003e\n\u003cp\u003eOn Sabouraud dextrose medium (Thermo, USA), the isolate exhibited pale yellow yeast colonies after incubation at 35\u0026deg;C for 72 hours. When cultured on\u0026nbsp;Candida chromogenic medium (CHROMagar, France), the colonies appeared blue to green in color (Supplementary Figure 1). Antifungal susceptibility testing was performed on the isolate using YeastOne Sensititre (Thermo, USA). After 48 hours of incubation, the MICs of the tested isolate were as follows: fluconazole 16 mg/L, itraconazole 0.25 mg/L, voriconazole 0.12 mg/L, posaconazole 0.25 mg/L, micafungin 0.03 mg/L, anidulafungin 0.03 mg/L, caspofungin 0.03 mg/L, flucytosine 0.5 mg/L, and amphotericin B 1 mg/L.\u003c/p\u003e\n\u003cp\u003eThe internal transcribed spacer (ITS) region of isolate 17G1312 was amplified and sequenced using ABI 3730xl platform (Thermo, USA). The strain\u0026rsquo;s sequence was 100% (576/576) identical to that of \u003cem\u003eC. mucifera\u003c/em\u003e strain 80408 (GenBank accession no. OR761613.1) and 99.5% (555/558) to \u003cem\u003eC. mucifera\u003c/em\u003e type strain CBS 7409\u003csup\u003eT\u003c/sup\u003e (GenBank accession no. NR_130678.1), but only 95.4% (554/581) similarity to \u003cem\u003eT. ciferrii\u0026nbsp;\u003c/em\u003etype strain CBS 5295\u003csup\u003eT\u003c/sup\u003e (GenBank accession no. NR_111160.1). The maximum likelihood tree constructed based on ITS region sequences, further support assigning the isolate 17G1312 as \u003cem\u003eC. mucifera\u003c/em\u003e (Supplementary Figure 2).\u003c/p\u003e\n\u003cp\u003eAs there was no publicly available genome information for \u003cem\u003eC. mucifera\u003c/em\u003e, we conducted whole-genome sequencing of the isolate 17G1312 using short-reads on the Illumina MiSeq PE150 (Illumina, USA) and long-reads on the PacBio Sequel II (PacBio, USA). The assembly process involved converting the BAM file to a FASTA file using SAMtools v1.9\u0026nbsp;[5], assembly using Flye v2.9.3\u0026nbsp;[6], and polishing the assembly results using Pilon v1.23,\u0026nbsp;with short reads filtered by fastp v0.23.4\u0026nbsp;[7, 8]. The genome completeness was assessed using BUSCO v5.2.2 and the saccharomycetes_odb10 database\u0026nbsp;[9], revealing an integrity of 96.2% (single-copy: 95.5%, duplicated: 0.7%). The genome of this new strain comprises 8 scaffolds with a total length of 16,402,853 bp (15.6 Mb). The N50 is 2,475,350 bp, and the GC content is 44.9%.\u003c/p\u003e\n\u003cp\u003eThe genome of isolate 17G1312 (GenBank assembly accession: GCA_036871495.1) was compared with two genomes of its closely-related species \u003cem\u003eT. ciferrii\u0026nbsp;\u003c/em\u003e(strains NRRL Y-10943 [GenBank assembly accession: GCA_030573635.1], and CBS 4856 [GenBank assembly accession: GCA_008704605.1]) using fastANI v1.33\u0026nbsp;[10], and the average nucleotide identity (ANI) between isolate 17G1312 and two \u003cem\u003eT. ciferrii\u0026nbsp;\u003c/em\u003estrains, was only 80.6%.\u0026nbsp;Gene annotation results of \u003cem\u003eT. ciferrii\u003c/em\u003e strain CBS 4856 were used to train a new de novo prediction model for AUGUSTUS v3.3.2 and then utilized for structural annotation of our \u003cem\u003eC. mucifera\u0026nbsp;\u003c/em\u003egenome\u0026nbsp;[11], and a total of 6533 genes were predicted.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eDue to the \u0026ldquo;intrinsically\u0026rdquo; reduced fluconazole susceptibility in \u003cem\u003eC. mucifera\u003c/em\u003e and other species of the \u003cem\u003eT. ciferrii\u0026nbsp;\u003c/em\u003ecomplex\u0026nbsp;[3], we conducted an mutation analysis of the azole target Erg11p. We observed that position 499 of Erg11p amino acid sequence in \u003cem\u003eC. mucifera\u003c/em\u003e isolate 17G1312 (GenBank accession no. PP204302.1), and the homologous position (position 501) in \u003cem\u003eT. ciferrii\u003c/em\u003e (GenBank accession no. PP213130.1), had a valine (V) residue. In contrast to this finding, in wild-type azole-susceptible \u003cem\u003eCandida albicans\u003c/em\u003e strains (e.g. strain no. SC5314, GenBank accession no. XP_716761.1), the homologous position of Erg11p at position 488 has an isoleucine (I) residue. Of note, the V488I amino acid substitution in \u003cem\u003eC. albicans\u0026nbsp;\u003c/em\u003ehas been reported to be responsible for fluconazole resistance\u0026nbsp;[12]. Consequently, we hypothesize that the V499I substitution in \u003cem\u003eC. mucifera\u0026nbsp;\u003c/em\u003eErg11p (corresponding to V501I substitution in \u003cem\u003eT. ciferrii\u003c/em\u003e) introduced reduced fluconazole susceptibility within this species complex.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eIn summary, we described (and deposited) the complete genome of a rare human yeast pathogen, \u003cem\u003eC. mucifera\u003c/em\u003e. In addition, our analysis provides a potential mechanism explanation for \u0026ldquo;intrinsically\u0026rdquo; reduced azole susceptibility in \u003cem\u003eTrichomonascus ciferrii-Candida mucifera\u003c/em\u003e species complex. The methodology used, as well as the availability of data and stock cultures, adheres to the quality assurance checklist of MycopathologiaGENOMES\u0026nbsp;[13].\u003c/p\u003e\n"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe isolate 17G1312 has been deposited at China General Microbiological Culture Collection Center under the accession number CGMCC2.8257. The \u003cem\u003eERG11\u003c/em\u003e, ITS, D1/D2 region of the isolate 17G1312 have been released in GenBank (accession nos. PP204302.1, PP204071.1, PP230918.1). All sequencing data have been deposited in the NCBI database (GenBank accession nos. CP145483.1-CP145490.1, assembly accession no. GCA_036871495.1, Biosample no. SAMN39602682, BioProject no. PRJNA1068766). \u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was financially supported by the National Key Research and Development Program of China (2022YFC2303002), and the National High Level Hospital Clinical Research Funding (2022-PUMCH-C-052).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eM. X. and Y.-C. X. conceived and planned the experiments. R.-C. D. and M. X. performed the genomic analysis. J. G., Y.-T. N., W. Z., X.-F. C. and G. Z. collected the isolate and clinical data. R.-C. D., Y.-T. N. and M. X. contributed to the first draft of the manuscript. J. G., T. K., and Y.-C. X. contributed to the review and editing.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was approved by the Human Research Ethics Committee of Peking Union Medical College Hospital (No. S-263).\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no relevant financial or non-financial interests to disclose.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eVisagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci\u0026apos;s yeast: \u003cem\u003eBlastobotrys davincii\u003c/em\u003e f.a., sp. nov. Yeast. 2023;40(1):7-31.\u003c/li\u003e\n\u003cli\u003eUeda-Nishimura K, Mikata K. Species distinction of the ascomycetous heterothallic yeast-like fungus \u003cem\u003eStephanoascus ciferrii\u003c/em\u003e complex: description of\u003cem\u003e Candida allociferrii\u003c/em\u003e sp. nov. and reinstatement of \u003cem\u003eCandida mucifera\u003c/em\u003e Kockova-Kratochvilova et Slavikova. Int J Syst Evol Microbiol. 2002;52(Pt 2):463-71.\u003c/li\u003e\n\u003cli\u003eGuo P, Wu Z, Liu P, Chen Y, Liao K, Peng Y, et al. Identification and Antifungal Susceptibility Analysis of \u003cem\u003eStephanoascus ciferrii\u003c/em\u003e Complex Species Isolated From Patients With Chronic Suppurative Otitis Media. Front Microbiol. 2021;12:680060.\u003c/li\u003e\n\u003cli\u003eShoubao Y, Jie Y, TingTing S, Jiaquan G, Cuie S. Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor. AMB Express. 2023;13(1):56.\u003c/li\u003e\n\u003cli\u003eLi H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 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Mol Biol Evol. 2021;38(10):4647-54.\u003c/li\u003e\n\u003cli\u003eJain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.\u003c/li\u003e\n\u003cli\u003eStanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008;24(5):637-44.\u003c/li\u003e\n\u003cli\u003eManastir L, Ergon MC, Yucesoy M. Investigation of mutations in \u003cem\u003eErg11\u003c/em\u003e gene of fluconazole resistant \u003cem\u003eCandida albicans\u003c/em\u003e isolates from Turkish hospitals. Mycoses. 2011;54(2):99-104.\u003c/li\u003e\n\u003cli\u003eMac Aogain M, Chaturvedi V, Chotirmall SH. MycopathologiaGENOMES: The New \u0026apos;Home\u0026apos; for the Publication of Fungal Genomes. Mycopathologia. 2019;184(5):551-4.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"mycopathologia","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"myco","sideBox":"Learn more about [Mycopathologia](https://www.springer.com/journal/11046)","snPcode":"11046","submissionUrl":"https://submission.nature.com/new-submission/11046/3","title":"Mycopathologia","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Candida mucifera, Fungal infection, Whole genome sequencing, Reduced azole susceptibility, Resistant mechanism","lastPublishedDoi":"10.21203/rs.3.rs-4134268/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4134268/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eWe describe for the first time, a high-quality genome for a rare human yeast pathogen \u003cem\u003eCandida mucifera\u003c/em\u003e, from a patient with chronic suppurative otitis media. Antifungal susceptibility profile was determined, and a potential mechanism responsible for intrinsically reduced azole susceptibility in \u003cem\u003eTrichomonascus ciferrii-Candida mucifera\u003c/em\u003e species complex was proposed.\u003c/p\u003e","manuscriptTitle":"Complete Genome Sequence of Candida mucifera from an Otitis Media Patient","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-04-29 08:46:40","doi":"10.21203/rs.3.rs-4134268/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Minor revisions","date":"2024-06-17T07:48:53+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2024-05-28T10:40:34+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-04-24T10:31:00+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"Mycopathologia","date":"2024-04-02T22:21:48+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-04-01T07:44:45+00:00","index":"","fulltext":""},{"type":"submitted","content":"Mycopathologia","date":"2024-03-31T21:02:05+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"mycopathologia","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"myco","sideBox":"Learn more about [Mycopathologia](https://www.springer.com/journal/11046)","snPcode":"11046","submissionUrl":"https://submission.nature.com/new-submission/11046/3","title":"Mycopathologia","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"807f21db-4205-4ed9-934c-d64a3791afac","owner":[],"postedDate":"April 29th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2024-09-09T16:18:12+00:00","versionOfRecord":{"articleIdentity":"rs-4134268","link":"https://doi.org/10.1007/s11046-024-00878-7","journal":{"identity":"mycopathologia","isVorOnly":false,"title":"Mycopathologia"},"publishedOn":"2024-09-02 16:08:28","publishedOnDateReadable":"September 2nd, 2024"},"versionCreatedAt":"2024-04-29 08:46:40","video":"","vorDoi":"10.1007/s11046-024-00878-7","vorDoiUrl":"https://doi.org/10.1007/s11046-024-00878-7","workflowStages":[]},"version":"v1","identity":"rs-4134268","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4134268","identity":"rs-4134268","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}