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Genome update of the dimorphic human pathogenic fungi causing Paracoccidioidomycosis

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dc.creatorMuñoz, José F.
dc.creatorGallo, Juan E.
dc.creatorMisas, Elizabeth
dc.creatorPriest, Margaret
dc.creatorImamovic, Alma
dc.creatorYoung, Sarah
dc.creatorZeng, Qiandong
dc.creatorClay, Oliver K.
dc.creatorMcEwen, Juan G.
dc.creatorCuomo, Christina A.
dc.creator.googleMuñoz, José F.spa
dc.creator.googleGallo, Juan E.spa
dc.creator.googleMisas, Elizabethspa
dc.creator.googlePriest, Margaretspa
dc.creator.googleImamovic, Almaspa
dc.creator.googleYoung, Sarahspa
dc.creator.googleZeng, Quiandongspa
dc.creator.googleClay, Oliver K.spa
dc.creator.googleMcEwen, Juan G.spa
dc.creator.googleCuomo, Christinaspa
dc.date.accessioned2020-04-22T02:23:59Z
dc.date.available2020-04-22T02:23:59Z
dc.date.created2014
dc.date.issued2014
dc.description.abstractParacoccidiodomycosis (PCM) is a clinically important fungal disease that can acquire serious systemic forms and is caused by the thermodimorphic fungal Paracoccidioides spp. PCM is a tropical disease that is endemic in Latin America, where up to ten million people are infected; 80% of reported cases occur in Brazil, followed by Colombia and Venezuela. To enable genomic studies and to better characterize the pathogenesis of this dimorphic fungus, two reference strains of P. brasiliensis (Pb03, Pb18) and one strain of P. lutzii (Pb01) were sequenced [1]. While the initial draft assemblies were accurate in large scale structure and had high overall base quality, the sequences had frequent small scale defects such as poor quality stretches, unknown bases (N's), and artifactual deletions or nucleotide duplications, all of which caused larger scale errors in predicted gene structures. Since assembly consensus errors can now be addressed using next generation sequencing (NGS) in combination with recent methods allowing systematic assembly improvement, we re-sequenced the three reference strains of Paracoccidioides spp. using Illumina technology. We utilized the high sequencing depth to re-evaluate and improve the original assemblies generated from Sanger sequence reads, and obtained more complete and accurate reference assemblies. The new assemblies led to improved transcript predictions for the vast majority of genes of these reference strains, and often substantially corrected gene structures. These include several genes that are central to virulence or expressed during the pathogenic yeast stage in Paracoccidioides and other fungi, such as HSP90, RYP1-3, BAD1, catalase B, alpha-1,3-glucan synthase and the beta glucan synthase target gene FKS1. The improvement and validation of these reference sequences will now allow more accurate genome-based analyses. To our knowledge, this is one of the first reports of a fully automated and quality-assessed upgrade of a genome assembly and annotation for a non-model fungus. © 2014 Muñoz et al.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1371/journal.pntd.0003348
dc.identifier.issn1935-2727
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/21730
dc.language.isoengspa
dc.relation.citationIssueNo. 12
dc.relation.citationTitlePLoS Neglected Tropical Diseases
dc.relation.citationVolumeVol. 8
dc.relation.ispartofPLoS Neglected Tropical Diseases, ISSN: 1935-2727 Vol. 8, No. 12 (2014)spa
dc.relation.urihttps://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0003348&type=printablespa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosario
dc.source.reponamereponame:Repositorio Institucional EdocUR
dc.subject.ddcEnfermedadesspa
dc.subject.keywordBeta glucan synthasespa
dc.subject.keywordBeta glucanosyltransferasespa
dc.subject.keywordHydroxyphenylpyruvate dioxygenasespa
dc.subject.keywordAdhesin WI 1spa
dc.subject.lembParacoccidioidomicosisspa
dc.subject.lembGenética humanaspa
dc.titleGenome update of the dimorphic human pathogenic fungi causing Paracoccidioidomycosisspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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