{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T05:08:52Z","timestamp":1773032932738,"version":"3.50.1"},"reference-count":87,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T00:00:00Z","timestamp":1643932800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Over the past decade, <jats:italic>Apiotrichum mycotoxinivorans<\/jats:italic> has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of <jats:italic>A. mycotoxinivorans<\/jats:italic> infections. Therefore, to investigate the genetic basis for the pathogenicity of <jats:italic>A. mycotoxinivorans<\/jats:italic>, we performed whole-genome sequencing and comparative genomic analysis of <jats:italic>A. mycotoxinivorans<\/jats:italic> GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that <jats:italic>A. mycotoxinivorans<\/jats:italic> exhibited the closest evolutionary affinity to <jats:italic>A. veenhuisii<\/jats:italic>, and both the <jats:italic>A. mycotoxinivorans<\/jats:italic> strains and the formerly <jats:italic>Trichosporon cutaneum<\/jats:italic> ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to <jats:italic>A. mycotoxinivorans<\/jats:italic>. Comparisons of three <jats:italic>A. mycotoxinivorans<\/jats:italic> strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the <jats:italic>Trichosporonaceae<\/jats:italic> family, we identified potential key genetic factors associated with <jats:italic>A. mycotoxinivorans<\/jats:italic> infection or pathogenicity. In addition, we also deduced that <jats:italic>A. mycotoxinivorans<\/jats:italic> had great potential to inactivate some antibiotics (<jats:italic>e.g.<\/jats:italic>, tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the <jats:italic>Trichosporonaceae<\/jats:italic> family, uncover the underlying genetic basis of <jats:italic>A. mycotoxinivorans<\/jats:italic> infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.<\/jats:p>","DOI":"10.3389\/fcimb.2022.834015","type":"journal-article","created":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T11:22:10Z","timestamp":1643973730000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709"],"prefix":"10.3389","volume":"12","author":[{"given":"Liang","family":"Peng","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen-Fei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hai","family":"Jin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Yan","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li-Ting","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cong","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi-Kai","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,2,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-59672-2","article-title":"Genomic Insights Into the Lifestyles, Functional Capacities and Oleagenicity of Members of the Fungal Family Trichosporonaceae","volume":"10","author":"Aliyu","year":"2020","journal-title":"Sci. Rep."},{"key":"B2","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1590\/0074-02760170011","article-title":"Emergence of Trichosporon Mycotoxinivorans (Apiotrichum Mycotoxinivorans) Invasive Infections in Latin America","volume":"112","author":"Almeida","year":"2017","journal-title":"Mem I Oswaldo Cruz"},{"key":"B3","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","article-title":"Mugsy: Fast Multiple Alignment of Closely Related Whole Genomes","volume":"27","author":"Angiuoli","year":"2010","journal-title":"Bioinformatics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"fov057","DOI":"10.1093\/femsyr\/fov057","article-title":"Review of Current Methods for Characterizing Virulence and Pathogenicity Potential of Industrial Saccharomyces Cerevisiae Strains Towards Humans","volume":"15","author":"Anoop","year":"2015","journal-title":"FEMS Yeast Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and Genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res."},{"key":"B7","doi-asserted-by":"publisher","first-page":"4.3.1","DOI":"10.1002\/0471250953.bi0403s18","article-title":"Using Geneid to Identify Genes","volume":"18","author":"Blanco","year":"2007","journal-title":"Curr. Protoc. Bioinf."},{"key":"B8","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1186\/s12864-021-07512-6","article-title":"Telomere-To-Telomere Assembly of the Genome of an Individual Oikopleura Dioica From Okinawa Using Nanopore-Based Sequencing","volume":"22","author":"Bliznina","year":"2021","journal-title":"BMC Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and Sensitive Protein Alignment Using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"B10","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of Complete Gene Structures in Human Genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. Mol. Biol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1038\/nbt.2727","article-title":"Chromosome-Scale Scaffolding of De Novo Genome Assemblies Based on Chromatin Interactions","volume":"31","author":"Burton","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"e01235","DOI":"10.1128\/genomeA.01235-16","article-title":"Draft Genome Sequence of the Oleaginous Yeast Cryptococcus Curvatus ATCC 20509","volume":"4","author":"Close","year":"2016","journal-title":"Genome Announcements"},{"key":"B13","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/mmy\/myw100","article-title":"Molecular and Antifungal Susceptibility Study on Trichosporonemia and Emergence of Trichosporon Mycotoxinivorans as a Bloodstream Pathogen","volume":"55","author":"Dabas","year":"2017","journal-title":"Med. Mycol"},{"key":"B14","first-page":"71","article-title":"Integrated Nr Database in Protein Annotation System and Its Localization","volume":"32","author":"Deng","year":"2006","journal-title":"Comput. Eng."},{"key":"B15","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1093\/femsre\/fuy008","article-title":"Bacterial-Fungal Interactions: Ecology, Mechanisms and Challenges","volume":"42","author":"Deveau","year":"2018","journal-title":"FEMS Microbiol. Rev."},{"key":"B16","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/s11046-019-00407-x","article-title":"Molecular Identification, Genotyping, Phenotyping, and Antifungal Susceptibilities of Medically Important Trichosporon, Apiotrichum, and Cutaneotrichosporon Species","volume":"185","author":"do Esp\u00edrito Santo","year":"2020","journal-title":"Mycopathologia"},{"key":"B17","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1007\/s12010-016-2332-0","article-title":"Solid Flocculation and Emulsifying Activities of the Lipopolysaccharide Produced by Trichosporon Mycotoxinivorans CLA2","volume":"182","author":"Domingues","year":"2017","journal-title":"Appl. Biochem. Biotech."},{"key":"B18","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/j.ymeth.2012.06.018","article-title":"A Genome-Wide 3C-Method for Characterizing the Three-Dimensional Architectures of Genomes","volume":"58","author":"Duan","year":"2012","journal-title":"Methods (San Diego Calif)"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple Sequence Alignment With High Accuracy and High Throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"4218","DOI":"10.1093\/nar\/27.21.4218","article-title":"Whole Genome-Based Phylogenetic Analysis of Free-Living Microorganisms","volume":"27","author":"Fitz-Gibbon","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1128\/MMBR.00020-11","article-title":"Bacterial-Fungal Interactions: Hyphens Between Agricultural, Clinical, Environmental, and Food Microbiologists","volume":"75","author":"Frey-Klett","year":"2011","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B22","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1007\/s13205-018-1465-y","article-title":"Genome-Wide Overview of Trichosporon Akiyoshidainum HP-2023, New Insights Into Its Mechanism of Dye Discoloration. 3","volume":"8","author":"Gil","year":"2018","journal-title":"Biotech"},{"key":"B23","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1186\/s12879-016-1910-7","article-title":"A Case Report of a Cystic Fibrosis Patient With Repeated Isolation of Trichosporon Mycotoxinivorans Identified by a Novel Short-Extraction Method","volume":"16","author":"Goldenberger","year":"2016","journal-title":"BMC Infect. Dis."},{"key":"B24","doi-asserted-by":"publisher","first-page":"11\u201313","DOI":"10.7150\/jgen.32210","article-title":"Draft Genome Sequence of the Oleaginous Yeast Apiotrichum Porosum (Syn. Trichosporon Porosum) DSM 27194","volume":"7","author":"Gorte","year":"2019","journal-title":"J. Genomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1471-2164-14-33","article-title":"Comparative Gene Expression Between Two Yeast Species","volume":"14","author":"Guan","year":"2013","journal-title":"BMC Genomics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De Novo Transcript Sequence Reconstruction From RNA-Seq Using the Trinity Platform for Reference Generation and Analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat. Protoc."},{"key":"B27","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1089\/jir.2015.0095","article-title":"Decreased Cell Wall Galactosaminogalactan in Aspergillus Nidulans Mediates Dysregulated Inflammation in the Chronic Granulomatous Disease Host","volume":"36","author":"Henriet","year":"2016","journal-title":"J. Interf. Cytok. Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"3091","DOI":"10.1128\/JCM.00460-09","article-title":"Trichosporon Mycotoxinivorans, a Novel Respiratory Pathogen in Patients With Cystic Fibrosis","volume":"47","author":"Hickey","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"4168","DOI":"10.1128\/JCM.01928-12","article-title":"Disseminated Trichosporon Mycotoxinivorans, Aspergillus Fumigatus, and Scedosporium Apiospermum Coinfection After Lung and Liver Transplantation in a Cystic Fibrosis Patient","volume":"50","author":"Hirschi","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"4279","DOI":"10.1080\/09593330.2020.1754472","article-title":"Optimization of Media Composition for Enhancing Tetracycline Degradation by Trichosporon Mycotoxinivorans XPY-10 Using Response Surface Methodology","volume":"42","author":"Huang","year":"2021","journal-title":"Environ. Technol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and Model-Centric Curation of the Comprehensive Antibiotic Resistance Database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B33","doi-asserted-by":"publisher","first-page":"e89","DOI":"10.1093\/nar\/gkw092","article-title":"Using Intron Position Conservation for Homology-Based Gene Prediction","volume":"44","author":"Keilwagen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.5897\/AJMR12.141","article-title":"Enzymatic Activity and Some Molecular Properties of Trichosporon Mycotoxinovorans Yeast and Their Effect on Liver Function in Mice","volume":"6","author":"Khalel","year":"2012","journal-title":"Afr J. Microbiol. Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"289","DOI":"10.5423\/PPJ.2010.26.3.289","article-title":"Simple and Reliable DNA Extraction Method for the Dark Pigmented Fungus, Cercospora Sojina","volume":"26","author":"Kim","year":"2010","journal-title":"Plant Pathol. J."},{"key":"B36","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: Scalable and Accurate Long-Read Assembly via Adaptive K-Mer Weighting and Repeat Separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"B37","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene Finding in Novel Genomes","volume":"5","author":"Korf","year":"2004","journal-title":"BMC Bioinf."},{"key":"B38","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting Transmembrane Protein Topology With a Hidden Markov Model: Application to Complete Genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"e1005187","DOI":"10.1371\/journal.ppat.1005187","article-title":"The Fungal Exopolysaccharide Galactosaminogalactan Mediates Virulence by Enhancing Resistance to Neutrophil Extracellular Traps","volume":"11","author":"Lee","year":"2015","journal-title":"PloS Pathog."},{"key":"B40","doi-asserted-by":"publisher","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree Of Life (iTOL) V4: Recent Updates and New Developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B41","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B42","doi-asserted-by":"publisher","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"B43","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.simyco.2015.07.001","article-title":"Towards an Integrated Phylogenetic Classification of the Tremellomycetes","volume":"81","author":"Liu","year":"2015","journal-title":"Stud. Mycol"},{"key":"B44","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"Trnascan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B45","doi-asserted-by":"publisher","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","article-title":"TigrScan and GlimmerHMM: Two Open Source Ab Initio Eukaryotic Gene-Finders","volume":"20","author":"Majoros","year":"2004","journal-title":"Bioinformatics"},{"key":"B46","first-page":"37","article-title":"A Trich-Y Fungus: A Unique Presentation of Disseminated Trichosporon Mycotoxinivorans Infection","volume":"8","author":"Marcelo","year":"2018","journal-title":"J. Pioneer Med. Sci."},{"key":"B47","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The Comprehensive Antibiotic Resistance Database","volume":"57","author":"McArthur","year":"2013","journal-title":"Antimicrob. Agents Ch."},{"key":"B48","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1078\/0723202042369947","article-title":"Trichosporon Mycotoxinivorans Sp. Nov., A New Yeast Species Useful in Biological Detoxification of Various Mycotoxins","volume":"27","author":"Molnar","year":"2004","journal-title":"Syst. Appl. Microbiol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"3233","DOI":"10.1093\/bioinformatics\/bty321","article-title":"MARDy: Mycology Antifungal Resistance Database","volume":"34","author":"Nash","year":"2018","journal-title":"Bioinformatics"},{"key":"B50","doi-asserted-by":"publisher","first-page":"D130","DOI":"10.1093\/nar\/gku1063","article-title":"Rfam 12.0: Updates to the RNA Families Database","volume":"43","author":"Nawrocki","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B51","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-Fold Faster RNA Homology Searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"B52","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/s00210-007-0131-4","article-title":"Phospholipase D Signaling: Orchestration by PIP2 and Small GTPases","volume":"374","author":"Oude Weernink","year":"2007","journal-title":"N-S Arch. Pharmacol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1038\/nrmicro2313","article-title":"Medically Important Bacterial\u2013Fungal Interactions","volume":"8","author":"Peleg","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.mycmed.2019.01.010","article-title":"Molecular Identification and Biological Characteristic Analysis of an Apiotrichum Mycotoxinivorans (Formerly Trichosporon Mycotoxinivorans) Strain Isolated From Sputum Specimens of a Pediatric Patient With Pneumonia","volume":"29","author":"Peng","year":"2019","journal-title":"J. Mycol. Med."},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.01522","article-title":"Opportunistic Strains of Saccharomyces Cerevisiae: A Potential Risk Sold in Food Products","volume":"6","author":"P\u00e9rez-Torrado","year":"2016","journal-title":"Front. Microbiol."},{"key":"B56","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-Level Expression Analysis of RNA-Seq Experiments With HISAT, StringTie and Ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat. Protoc."},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2020.00117","article-title":"Origin, Diversity, and Evolution of Telomere Sequences in Plants","volume":"11","author":"Peska","year":"2020","journal-title":"Front. Plant Sci."},{"key":"B58","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/nmeth.1701","article-title":"SignalP 4.0: Discriminating Signal Peptides From Transmembrane Regions","volume":"8","author":"Petersen","year":"2011","journal-title":"Nat. Methods"},{"key":"B59","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/bs.mim.2015.05.002","article-title":"Invasive Fungal Infections and Approaches to Their Diagnosis","volume":"42","author":"Pfaller","year":"2015","journal-title":"Method Microbiol."},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.676751","article-title":"Telomere Roles in Fungal Genome Evolution and Adaptation","volume":"12","author":"Rahnama","year":"2021","journal-title":"Front. Genet."},{"key":"B61","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.ympev.2017.07.009","article-title":"Inferring the Shallow Phylogeny of True Salamanders (Salamandra) by Multiple Phylogenomic Approaches","volume":"115","author":"Rodr\u00edguez","year":"2017","journal-title":"Mol. Phylogenet. Evol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","article-title":"Fast and Accurate Long-Read Assembly With Wtdbg2","volume":"17","author":"Ruan","year":"2020","journal-title":"Nat. Methods"},{"key":"B63","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1016\/j.jiac.2020.03.002","article-title":"A Rare Case of Trichosporon Mycotoxinivorans and Cryptococcus Neoformans Co-Infection in Lung","volume":"26","author":"Sadamatsu","year":"2020","journal-title":"J. Infect. Chemother."},{"key":"B64","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.ejbt.2020.01.009","article-title":"Single Cell Oil Production by a Novel Yeast Trichosporon Mycotoxinivorans for Complete and Ecofriendly Valorization of Paddy Straw","volume":"44","author":"Sagia","year":"2020","journal-title":"Electron J. Biotechn."},{"key":"B65","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1007\/BF02942950","article-title":"Investigation of Different Yeast Strains for the Detoxification of Ochratoxin A","volume":"19","author":"Schatzmayr","year":"2003","journal-title":"Mycotoxin Res."},{"key":"B66","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-Pro: An Optimized and Flexible Pipeline for Hi-C Data Processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1089\/ind.2016.0011","article-title":"The Generally Recognized as Safe (GRAS) Process for Industrial Microbial Enzymes","volume":"12","author":"Sewalt","year":"2016","journal-title":"Ind. Biotechnol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"2242","DOI":"10.1128\/JCM.03309-13","article-title":"Trichosporon Mycotoxinivorans Infection in Patients With Cystic Fibrosis","volume":"52","author":"Shah","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1101\/gr.082081.108","article-title":"GenBlastA: Enabling BLAST to Identify Homologous Gene Sequences","volume":"19","author":"She","year":"2009","journal-title":"Genome Res."},{"key":"B70","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing Genome Assembly and Annotation Completeness With Single-Copy Orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"B71","unstructured":"SmitA.\n            HubleyR.\n            GreenP.\n          RepeatModeler Open-1.0 (2008-2015)2015"},{"key":"B72","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1080\/21505594.2019.1568174","article-title":"Galactosamino-Galactan (GAG) and Its Multiple Roles in Aspergillus Pathogenesis","volume":"10","author":"Speth","year":"2019","journal-title":"Virulence"},{"key":"B73","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML Version 8: A Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"B74","doi-asserted-by":"publisher","first-page":"ii215","DOI":"10.1093\/bioinformatics\/btg1080","article-title":"Gene Prediction With a Hidden Markov Model and a New Intron Submodel","volume":"19","author":"Stanke","year":"2003","journal-title":"Bioinformatics"},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01866","article-title":"Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum Mycotoxinivorans: Predicting Putative Zearalenone-Degradation Enzymes","volume":"11","author":"Sun","year":"2020","journal-title":"Front. Microbiol."},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.31631","article-title":"Jcvi: JCVI Utility Libraries","author":"Tang","year":"2015","journal-title":"Zenodo"},{"key":"B77","doi-asserted-by":"publisher","first-page":"4.10.1","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr. Protoc. Bioinf."},{"key":"B78","doi-asserted-by":"publisher","first-page":"D613","DOI":"10.1093\/nar\/gkz904","article-title":"PHI-Base: The Pathogen-Host Interactions Database","volume":"48","author":"Urban","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B79","doi-asserted-by":"publisher","first-page":"D645","DOI":"10.1093\/nar\/gku1165","article-title":"The Pathogen-Host Interactions Database (PHI-Base): Additions and Future Developments","volume":"43","author":"Urban","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B80","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1016\/j.tig.2020.08.006","article-title":"Horizontal Gene Transfer in Eukaryotes: Not If, But How Much","volume":"36","author":"Van Etten","year":"2020","journal-title":"Trends Genet."},{"key":"B81","doi-asserted-by":"publisher","first-page":"5331","DOI":"10.1093\/nar\/gkv424","article-title":"Accurate Identification of Centromere Locations in Yeast Genomes Using Hi-C","volume":"43","author":"Varoquaux","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B82","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-1-4939-6622-6_1","article-title":"Genome Sequencing","volume":"1525","author":"Verma","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"B83","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PloS One"},{"key":"B84","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.jbiotec.2016.04.043","article-title":"Genome Sequence of Trichosporon Cutaneum ACCC 20271: An Oleaginous Yeast With Excellent Lignocellulose Derived Inhibitor Tolerance","volume":"228","author":"Wang","year":"2016","journal-title":"J. Biotechnol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1016\/j.bbrc.2018.09.157","article-title":"Aspergillus Fumigatus Phospholipase D may Enhance Reactive Oxygen Species Production by Accumulation of Histone Deacetylase 6","volume":"505","author":"Yu","year":"2018","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2016.00023","article-title":"Streptococcus Pneumoniae Endopeptidase O (PepO) Elicits a Strong Innate Immune Response in Mice via TLR2 and TLR4 Signaling Pathways","volume":"6","author":"Zhang","year":"2016","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B87","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-15-S10-P16","article-title":"Heatmap3: An Improved Heatmap Package With More Powerful and Convenient Features","volume":"15","author":"Zhao","year":"2014","journal-title":"BMC Bioinf."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2022.834015\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T11:22:19Z","timestamp":1643973739000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2022.834015\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,4]]},"references-count":87,"alternative-id":["10.3389\/fcimb.2022.834015"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2022.834015","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,4]]},"article-number":"834015"}}