{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T20:58:30Z","timestamp":1790456310645,"version":"4.1.0"},"reference-count":130,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2014,8,14]],"date-time":"2014-08-14T00:00:00Z","timestamp":1407974400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1004496","type":"journal-article","created":{"date-parts":[[2014,8,14]],"date-time":"2014-08-14T18:15:44Z","timestamp":1408040144000},"page":"e1004496","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":86,"title":["Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)"],"prefix":"10.1371","volume":"10","author":[{"given":"Volker U.","family":"Schwartze","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sascha","family":"Winter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina","family":"Shelest","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Marcet-Houben","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian","family":"Horn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Wehner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f6rg","family":"Linde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vito","family":"Valiante","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Sammeth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin","family":"Riege","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minou","family":"Nowrousian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Kaerger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilse D.","family":"Jacobsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Axel A.","family":"Brakhage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"B\u00f6cker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Voigt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,8,14]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.mycres.2007.03.004","article-title":"A higher-level phylogenetic classification of the Fungi","volume":"111","author":"DS Hibbett","year":"2007","journal-title":"Mycol Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1086\/432579","article-title":"Epidemiology and outcome of zygomycosis: a review of 929 reported cases","volume":"41","author":"MM Roden","year":"2005","journal-title":"Clin Infect Dis"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"S126","DOI":"10.1093\/clinids\/14.Supplement_1.S126","article-title":"Mucormycosis","volume":"14 Suppl 1","author":"M Sugar A","year":"1992","journal-title":"Clin Infect Dis"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1128\/CMR.13.2.236-301.2000","article-title":"Zygomycetes in human disease","volume":"13","author":"JA Ribes","year":"2000","journal-title":"Clin Microbiol Rev"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1080\/13693780500464930","article-title":"The rising trend of invasive zygomycosis in patients with uncontrolled diabetes mellitus","volume":"44","author":"A Chakrabarti","year":"2006","journal-title":"Med Mycol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1111\/j.1469-0691.2009.02985.x","article-title":"Current experience in treating invasive zygomycosis with posaconazole treatment options for zygomycosis","volume":"15","author":"OA Cornely","year":"2009","journal-title":"Clin Microbiol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1111\/j.1469-0691.2010.03456.x","article-title":"Zygomycosis in Europe: analysis of 230 cases accrued by the registry of the European Confederation of Medical Mycology (ECMM) Working Group on Zygomycosis between 2005 and 2007","volume":"17","author":"A Skiada","year":"2011","journal-title":"Clin Microbiol Infect"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1128\/JCM.06133-11","article-title":"Antifungal susceptibility and phylogeny of opportunistic members of the order mucorales","volume":"50","author":"RG Vitale","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1128\/JCM.06611-11","article-title":"Evidence implicating <italic>Thamnostylum lucknowense<\/italic> as an etiological agent of rhino-orbital mucormycosis","volume":"50","author":"I Xess","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1093\/cid\/cir880","article-title":"A global analysis of mucormycosis in France: The RetroZygo Study (2005\u20132007)","volume":"54","author":"F Lanternier","year":"2012","journal-title":"Clin Infect Dis"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1128\/JCM.00036-09","article-title":"Spectrum of zygomycete species identified in clinically significant specimens in the United States","volume":"47","author":"E Alvarez","year":"2009","journal-title":"J Clin Microbiol"},{"key":"ref12","first-page":"312","article-title":"Troisi\u00e9me m\u00e9moire sur les Mucorin\u00e9es","volume":"4","author":"Tieghem","year":"1876","journal-title":"Ann des Sci Nat Bot"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1016\/j.mycres.2007.07.002","article-title":"Revision of the genus <italic>Absidia<\/italic> (Mucorales, Zygomycetes) based on physiological, phylogenetic, and morphological characters; thermotolerant <italic>Absidia<\/italic> spp. form a coherent group, Mycocladiaceae fam. nov","volume":"111","author":"K Hoffmann","year":"2007","journal-title":"Mycol Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1128\/JCM.01744-09","article-title":"Species recognition and clinical relevance of the zygomycetous genus <italic>Lichtheimia<\/italic> (syn. <italic>Absidia<\/italic> pro parte, <italic>Mycocladus<\/italic>)","volume":"48","author":"A Alastruey-Izquierdo","year":"2010","journal-title":"J Clin Microbiol"},{"key":"ref15","unstructured":"De Hoog, GS, Guarro, J, Gene, J, Figueras M (2000) Atlas of Clinical Fungi. 2nd ed. Centraalbureau voor Schimmelcultures. p. 58\u2013114."},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1128\/JB.92.4.1236-1244.1966","article-title":"Control of dimorphism in <italic>Mucor rouxii<\/italic>","volume":"92","author":"CW Haidle","year":"1966","journal-title":"J Bacteriol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/BF00437243","article-title":"A case of pseudoparacoccidioidomycosis: Detection of the yeast phase of <italic>Mucor circinelloides<\/italic> in a clinical specimen Abstract","volume":"97","author":"BH Cooper","year":"1987","journal-title":"Mycopathologia"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"390","DOI":"10.2307\/3793195","article-title":"Anaerobic growth of molds isolated from fermentation starters used for foods in Asian countries","volume":"77","author":"CW Hesseltine","year":"1985","journal-title":"Mycologia"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2166","DOI":"10.1111\/j.1600-6143.2009.02754.x","article-title":"Pulmonary zygomycosis in solid organ transplant recipients in the current era","volume":"9","author":"H-Y Sun","year":"2009","journal-title":"Am J Transplant"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"981","DOI":"10.3109\/13693781003713711","article-title":"New evidence of the involvement of <italic>Lichtheimia corymbifera<\/italic> in farmer&apos;s lung disease","volume":"48","author":"A-P Bellanger","year":"2010","journal-title":"Med Mycol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1016\/j.fm.2011.08.005","article-title":"Mycobiota of cocoa: from farm to chocolate","volume":"28","author":"MV Copetti","year":"2011","journal-title":"Food Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"96","DOI":"10.4315\/0362-028X-67.1.96","article-title":"Fungi, aflatoxins, and cyclopiazonic acid associated with peanut retailing in Botswana","volume":"67","author":"FA Mphande","year":"2004","journal-title":"J Food Prot"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1016\/j.nbt.2011.05.004","article-title":"Fungi isolated from olive ecosystems and screening of their potential biotechnological use","volume":"29","author":"MA Baffi","year":"2012","journal-title":"N Biotechnol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1007\/s12275-012-1437-6","article-title":"Zygomycota associated with traditional meju, a fermented soybean starting material for soy sauce and soybean paste","volume":"50","author":"S Hong","year":"2012","journal-title":"J Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e40908","DOI":"10.1371\/journal.pone.0040908","article-title":"<italic>Lichtheimia<\/italic> species exhibit differences in virulence potential","volume":"7","author":"VU Schwartze","year":"2012","journal-title":"PLoS One"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e28319","DOI":"10.1371\/journal.pone.0028319","article-title":"Genome characterization of the oleaginous fungus <italic>Mortierella alpina<\/italic>","volume":"6","author":"L Wang","year":"2011","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s00294-002-0306-y","article-title":"Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution","volume":"41","author":"J W\u00f6stemeyer","year":"2002","journal-title":"Curr Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1000549","DOI":"10.1371\/journal.pgen.1000549","article-title":"Genomic analysis of the basal lineage fungus <italic>Rhizopus oryzae<\/italic> reveals a whole-genome duplication","volume":"5","author":"L-J Ma","year":"2009","journal-title":"PLoS Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/sj.hdy.6800789","article-title":"RNAi: a defensive RNA-silencing against viruses and transposable elements","volume":"96","author":"N Buchon","year":"2006","journal-title":"Heredity (Edinb)"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e1000458","DOI":"10.1371\/journal.ppat.1000458","article-title":"Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations","volume":"5","author":"TY James","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/nature10158","article-title":"Genome sequence and analysis of the tuber crop potato","volume":"475","author":"X Xu","year":"2011","journal-title":"Nature"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"45","DOI":"10.3109\/10409238409110269","article-title":"Processing of tRNA in prokaryotes and eukaryotes","volume":"17","author":"MP Deutscher","year":"1984","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1261\/rna.2130705","article-title":"A surprisingly large RNase P RNA in <italic>Candida glabrata<\/italic>","volume":"11","author":"R Kachouri","year":"2005","journal-title":"RNA"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"7935","DOI":"10.1128\/MCB.13.12.7935","article-title":"Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in <italic>Saccharomyces cerevisiae<\/italic>","volume":"13","author":"ME Schmitt","year":"1993","journal-title":"Mol Cell Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1083\/jcb.91.2.545","article-title":"Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein","volume":"91","author":"P Walter","year":"1981","journal-title":"J Cell Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1016\/j.tig.2007.09.001","article-title":"The expanding RNA polymerase III transcriptome","volume":"23","author":"G Dieci","year":"2007","journal-title":"Trends Genet"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve <italic>de novo<\/italic> gene finding","volume":"24","author":"M Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"A Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"D556","DOI":"10.1093\/nar\/gkq1109","article-title":"PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions","volume":"39","author":"J Huerta-Cepas","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1186\/gb-2008-9-10-235","article-title":"Large-scale assignment of orthology: back to phylogenetics?","volume":"9","author":"T Gabald\u00f3n","year":"2008","journal-title":"Genome Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/nrg1603","article-title":"Phylogenomics and the reconstruction of the tree of life","volume":"6","author":"F Delsuc","year":"2005","journal-title":"Nat Rev Genet"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/btn230","article-title":"DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony","volume":"24","author":"A Wehe","year":"2008","journal-title":"Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1089\/cmb.2009.0098","article-title":"Computation of median gene clusters","volume":"16","author":"S B\u00f6cker","year":"2009","journal-title":"J Comput Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1089\/cmb.2011.0132","article-title":"Efficient computation of approximate gene clusters based on reference occurrences","volume":"18","author":"K Jahn","year":"2011","journal-title":"J Comput Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1186\/1471-2148-9-295","article-title":"Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence","volume":"9","author":"M Marcet-Houben","year":"2009","journal-title":"BMC Evol Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1471-2105-11-24","article-title":"ETE: a python Environment for Tree Exploration","volume":"11","author":"J Huerta-Cepas","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D290","DOI":"10.1093\/nar\/gkr1065","article-title":"The Pfam protein families database","volume":"40","author":"M Punta","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"RD Finn","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"e283","DOI":"10.1371\/journal.pone.0000283","article-title":"Genesis of a Fungal Non-Self Recognition Repertoire","author":"M Paoletti","year":"2007","journal-title":"PlosOne"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1128\/AAC.01270-09","article-title":"Antifungal susceptibility profile of human-pathogenic species of <italic>Lichtheimia<\/italic>","volume":"54","author":"A Alastruey-Izquierdo","year":"2010","journal-title":"Antimicrob Agents Chemother"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1471-2229-4-10","article-title":"The roles of segmental and tandem gene duplication in the evolution of large gene families in <italic>Arabidopsis thaliana<\/italic>","volume":"4","author":"SB Cannon","year":"2004","journal-title":"BMC Plant Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1104\/pp.108.122457","article-title":"Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli","volume":"148","author":"K Hanada","year":"2008","journal-title":"Plant Physiol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gkj117","article-title":"Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the <italic>Saccharomyces cerevisiae<\/italic> genome","volume":"34","author":"JE Hirschman","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/nar\/gkl924","article-title":"Different levels of alternative splicing among eukaryotes","volume":"35","author":"E Kim","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"e1003376","DOI":"10.1371\/journal.pgen.1003376","article-title":"Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes","volume":"9","author":"AN Marshall","year":"2013","journal-title":"PLoS Genet"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1084\/jem.20041242","article-title":"Siderophore biosynthesis but not reductive iron assimilation is essential for <italic>Aspergillus fumigatus<\/italic> virulence","volume":"200","author":"M Schrettl","year":"2004","journal-title":"J Exp Med"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1126\/science.288.5468.1062","article-title":"A High-Affinity iron permease essential for <italic>Candida albicans<\/italic> virulence","volume":"288","author":"N Ramanan","year":"2000","journal-title":"Science (80-)"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1128\/CMR.12.3.394","article-title":"Acquisition, transport, and storage of iron by pathogenic fungi","volume":"12","author":"DH Howard","year":"1999","journal-title":"Clin Microbiol Rev"},{"key":"ref59","first-page":"169","article-title":"Cloning and functional characterization of the <italic>Rhizopus oryzae<\/italic> high affinity iron permease (rFTR1) gene","volume":"235","author":"Y Fu","year":"2004","journal-title":"FEMS Microbiol Lett"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1111\/j.1365-2958.2010.07234.x","article-title":"The high affinity iron permease is a key virulence factor required for <italic>Rhizopus oryzae<\/italic> pathogenesis","volume":"77","author":"AS Ibrahim","year":"2010","journal-title":"Mol Microbiol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1111\/j.1469-0691.2009.02976.x","article-title":"The role of iron and iron chelators in zygomycosis","volume":"15 Suppl 5","author":"aS Symeonidis","year":"2009","journal-title":"Clin Microbiol Infect"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/cid\/cir865","article-title":"Pathogenesis of Mucormycosis","volume":"54","author":"AS Ibrahim","year":"2012","journal-title":"Clin Infect Dis"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1111\/j.1365-2958.2011.07704.x","article-title":"Functional characterization of the ferroxidase, permease high-affinity iron transport complex from <italic>Candida albicans<\/italic>","volume":"81","author":"L Ziegler","year":"2011","journal-title":"Mol Microbiol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1111\/j.1574-6968.1992.tb05285.x","article-title":"Rhizoferrin: a complexone type siderophore of the Mucorales and entomophthorales (Zygomycetes)","volume":"73","author":"a Thieken","year":"1992","journal-title":"FEMS Microbiol Lett"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/BF01569891","article-title":"The carboxylate type siderophore rhizoferrin and its analogs produced by directed fermentation","volume":"14","author":"H Drechsel","year":"1995","journal-title":"J Ind Microbiol Microbiol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1172\/JCI116419","article-title":"Mucormycosis during deferoxamine therapy is a siderophore-mediated infection: <italic>In vitro<\/italic> and <italic>in vivo<\/italic> animal studies","volume":"91","author":"JR Boelaert","year":"1993","journal-title":"J Clin Invest"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"2649","DOI":"10.1172\/JCI32338","article-title":"The iron chelator deferasirox protects mice from mucormycosis through iron starvation","volume":"117","author":"AS Ibrahim","year":"2007","journal-title":"J Clin Invest"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/ismej.2008.19","article-title":"Evolution of host resistance in a toxin-producing bacterial-fungal alliance","volume":"2","author":"I Schmitt","year":"2008","journal-title":"ISME J"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1128\/AEM.01784-06","article-title":"Rhizonin, the first mycotoxin isolated from the zygomycota, is not a fungal metabolite but is produced by bacterial endosymbionts","volume":"73","author":"LP Partida-Martinez","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref70","article-title":"Siderophore production by pathogenic Mucorales and uptake of deferoxamine B","author":"G Larcher","year":"2013","journal-title":"Mycopathologia"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0014-5793(96)00667-9","article-title":"Fungal ferritins: the ferritin from mycelia of <italic>Absidia spinosa<\/italic> is a bacterioferritin","volume":"390","author":"CJ Carrano","year":"1996","journal-title":"FEBS Lett"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1741-7007-10-47","article-title":"Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi","volume":"10","author":"S Capella-Gutierrez","year":"2012","journal-title":"BMC Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1146\/annurev.phyto.45.062806.094338","article-title":"Siderophores in fungal physiology and virulence","volume":"46","author":"H Haas","year":"2008","journal-title":"Annu Rev Phytopathol"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"49","DOI":"10.3389\/fmicb.2011.00049","article-title":"The homeostasis of iron, copper, and zinc in paracoccidioides brasiliensis, <italic>Cryptococcus neoformans<\/italic> var. <italic>grubii<\/italic>, and <italic>Cryptococcus gattii<\/italic>: a comparative analysis","volume":"2","author":"MG Silva","year":"2011","journal-title":"Front Microbiol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"28","DOI":"10.3389\/fmicb.2012.00028","article-title":"Iron - a key nexus in the virulence of <italic>Aspergillus fumigatus<\/italic>","volume":"3","author":"H Haas","year":"2012","journal-title":"Front Microbiol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1128\/EC.05274-11","article-title":"SRE1 regulates iron-dependent and -independent pathways in the fungal pathogen <italic>Histoplasma capsulatum<\/italic>","volume":"11","author":"LH Hwang","year":"2012","journal-title":"Eukaryot Cell"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1080\/mmy.40.1.61.71","article-title":"Molecular cloning of an extracellular aspartic proteinase from <italic>Rhizopus microsporus<\/italic> and evidence for its expression during infection","volume":"40","author":"C Schoen","year":"2002","journal-title":"Med Mycol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1080\/13693780600936399","article-title":"Characterization of an extracellular subtilisin protease of <italic>Rhizopus microsporus<\/italic> and evidence for its expression during invasive rhinoorbital mycosis","volume":"44","author":"A Spreer","year":"2006","journal-title":"Med Mycol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1111\/j.1439-0507.2005.01165.x","article-title":"Hydrolytic enzymes as virulence factors of <italic>Candida albicans<\/italic>","volume":"48","author":"M Schaller","year":"2005","journal-title":"Mycoses"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"e1003350","DOI":"10.1371\/journal.ppat.1003350","article-title":"Global expression profiling of transcription factor genes provides new insights into pathogenicity and stress responses in the rice blast fungus","volume":"9","author":"S-Y Park","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1111\/j.1574-6968.2008.01293.x","article-title":"Transcription factors in fungi","volume":"286","author":"E Shelest","year":"2008","journal-title":"FEMS Microbiol Lett"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/S1360-1385(00)01600-9","article-title":"The WRKY superfamily of plant transcription factors","volume":"5","author":"T Eulgem","year":"2000","journal-title":"Trends Plant Sci"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1128\/MMBR.00005-10","article-title":"The evolution of sex: a perspective from the fungal kingdom","volume":"74","author":"SC Lee","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0378-1119(03)00747-9","article-title":"Role of MADS box proteins and their cofactors in combinatorial control of gene expression and cell development","volume":"316","author":"F Messenguy","year":"2003","journal-title":"Gene"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/nrg2847","article-title":"Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation","volume":"11","author":"JA Goodrich","year":"2011","journal-title":"Nat Rev Genet"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"e1003163","DOI":"10.1371\/journal.ppat.1003163","article-title":"Surviving the heat of the moment: a fungal pathogens perspective","volume":"9","author":"MD Leach","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1111\/j.1574-6968.1994.tb06699.x","article-title":"Microorganisms surviving for 5300 years","volume":"116","author":"K Haselwandter","year":"1994","journal-title":"FEMS Microbiol Lett"},{"key":"ref88","first-page":"45","article-title":"Genome sequence assembly using trace signals and additional sequence information","author":"B Chevreux","year":"1999","journal-title":"Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/1471-2105-8-64","article-title":"Minimus: a fast, lightweight genome assembler","volume":"8","author":"DD Sommer","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase Update, a database of eukaryotic repetitive elements","volume":"110","author":"J Jurka","year":"2005","journal-title":"Cytogenet Genome Res"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1186\/1471-2105-7-474","article-title":"Annotation, submission and screening of repetitive elements in Repbase: Repbase Submitter and Censor","volume":"7","author":"O Kohany","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"TM Lowe","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"K Lagesen","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkq1129","article-title":"Rfam: Wikipedia, clans and the \u201cdecimal\u201d release","volume":"39","author":"PP Gardner","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","article-title":"Infernal 1.0: inference of RNA alignments","volume":"25","author":"EP Nawrocki","year":"2009","journal-title":"Bioinformatics"},{"key":"ref98","first-page":"325","article-title":"Pattern searching\/alignment with RNA primary and secondary structures: an effective descriptor for tRNA","volume":"6","author":"D Gautheret","year":"1990","journal-title":"CABIOS"},{"key":"ref99","first-page":"28","article-title":"Fitting a mixture model by exceptation maximization to discover motifs in biopolymers","author":"TL Timothy","year":"1994","journal-title":"Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1093\/bioinformatics\/btn364","article-title":"EPoS: a modular software framework for phylogenetic analysis","volume":"24","author":"T Griebel","year":"2008","journal-title":"Bioinformatics"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ygeno.2011.05.009","article-title":"Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies","volume":"98","author":"Y Kong","year":"2011","journal-title":"Genomics"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome Biol"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1111\/j.1432-1033.1985.tb08671.x","article-title":"Strain-dependent variation in ribosomal DNA arrangement in <italic>Absidia glauca<\/italic>","volume":"146","author":"J W\u00f6stemeyer","year":"1985","journal-title":"Eur J Biochem"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment","volume":"33","author":"K Katoh","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1093\/molbev\/msm060","article-title":"Heads or tails: a simple reliability check for multiple sequence alignments","volume":"24","author":"G Landan","year":"2007","journal-title":"Mol Biol Evol"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1093\/nar\/gkl091","article-title":"M-Coffee: combining multiple sequence alignment methods with T-Coffee","volume":"34","author":"IM Wallace","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/oxfordjournals.molbev.a025808","article-title":"BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data","volume":"14","author":"O Gascuel","year":"1997","journal-title":"Mol Biol Evol"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"S Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"ref112","first-page":"267","article-title":"Information theory and extension of the maximum likelihood principle","author":"H Akaike","year":"1973","journal-title":"Proceedings of the 2nd international symposium on information theory"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"SQ Le","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/978-1-59745-515-2_12","article-title":"Gecko and GhostFam","author":"T Schmidt","year":"2007","journal-title":"Methods in Molecular Biology"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nature04332","article-title":"Genomic sequence of the pathogenic and allergenic filamentous fungus <italic>Aspergillus fumigatus<\/italic>","volume":"438","author":"WC Nierman","year":"2005","journal-title":"Nature"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1038\/nature04341","article-title":"Sequencing of <italic>Aspergillus nidulans<\/italic> and comparative analysis with <italic>A. fumigatus<\/italic> and <italic>A. oryzae<\/italic>","volume":"438","author":"JE Galagan","year":"2005","journal-title":"Nature"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/35106579","article-title":"Genome sequence and gene compaction of the eukaryote parasite <italic>Encephalitozoon cuniculi<\/italic>","volume":"414","author":"MD Katinka","year":"2001","journal-title":"Nature"},{"key":"ref118","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/nature724","article-title":"Genome sequence of <italic>Schizosaccharomyces pombe<\/italic>","volume":"415","author":"V Wood","year":"2002","journal-title":"Nature"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"e1000466","DOI":"10.1371\/journal.ppat.1000466","article-title":"Genomic analyses of the microsporidian <italic>Nosema ceranae<\/italic>, an emergent pathogen of honey bees","volume":"5","author":"RS Cornman","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref120","first-page":"2478","article-title":"Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth:","author":"CA Cuomo","year":"2012"},{"key":"ref121","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1019315108","article-title":"Obligate biotrophy features unraveled by the genomic analysis of rust fungi","author":"S Duplessis","year":"2011"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"11889","DOI":"10.1073\/pnas.1003391107","article-title":"Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom <italic>Coprinopsis cinerea<\/italic> (<italic>Coprinus cinereus<\/italic>)","volume":"107","author":"JE Stajich","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nbt967","article-title":"Genome sequence of the lignocellulose degrading fungus <italic>Phanerochaete chrysosporium<\/italic> strain RP78","volume":"22","author":"D Martinez","year":"2004","journal-title":"Nat Biotechnol"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nature06556","article-title":"The genome of <italic>Laccaria bicolor<\/italic> provides insights into mycorrhizal symbiosis","volume":"452","author":"F Martin","year":"2008","journal-title":"Nature"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1126\/science.1139158","article-title":"Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization","volume":"317","author":"NH Putnam","year":"2007","journal-title":"Science"},{"key":"ref126","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1038\/nature06617","article-title":"The genome of the choanoflagellate <italic>Monosiga brevicollis<\/italic> and the origin of metazoans","volume":"451","author":"N King","year":"2008","journal-title":"Nature"},{"key":"ref127","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1126\/science.1205411","article-title":"The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi","volume":"333","author":"DC Eastwood","year":"2011","journal-title":"Science"},{"key":"ref128","doi-asserted-by":"crossref","first-page":"e1002338","DOI":"10.1371\/journal.ppat.1002338","article-title":"Genomic transition to pathogenicity in chytrid fungi","volume":"7","author":"S Joneson","year":"2011","journal-title":"PLoS Pathog"},{"key":"ref129","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nature01554","article-title":"The genome sequence of the filamentous fungus <italic>Neurospora crassa<\/italic>","volume":"422","author":"JE Galagan","year":"2003","journal-title":"Nature"},{"key":"ref130","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/bti191","article-title":"RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees","volume":"21","author":"a Stamatakis","year":"2005","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1006491","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2016,12,5]],"date-time":"2016-12-05T00:00:00Z","timestamp":1480896000000}}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1004496","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,23]],"date-time":"2020-08-23T07:14:23Z","timestamp":1598166863000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1004496"}},"subtitle":[],"editor":[{"given":"Ashraf S.","family":"Ibrahim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,8,14]]},"references-count":130,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2014,8,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1004496","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pgen.1006491","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,14]]}}}