A gene atlas for human pathogenic fungi.

Keatinge Clay, Oliver

Publication:
A gene atlas for human pathogenic fungi.

dc.contributor.author	Keatinge Clay, Oliver
dc.contributor.corporatename	Universidad Colegio Mayor de Nuestra Señora del Rosario (Bogotá, Colombia)	spa
dc.coverage.projectdates	2013-2017	spa
dc.date.accessioned	2020-10-23T13:26:32Z
dc.date.accessioned	2020-12-17T23:52:18Z
dc.date.available	2020-10-23T13:26:32Z
dc.date.available	2020-12-17T23:52:18Z
dc.date.issued	2017-05-19
dc.description.abstract	In recent years there has been a dramatic increase in the number of fully sequenced and annotated unicellular fungi. Many of these fungi are human pathogenic fungi, and a major motivation for their sequencing was a need to ultimately have a reliable set of protein-coding genes, and their DNA and encoded protein sequences. Unfortunately, in a number of the medically important fungal species and their sequenced strains, the quality of the genes' protein-coding sequences, and the automated predictions of exactly where they are located on the chromosomal sequence or contig (coordinates of start, stop, and exon/intron boundaries) are not yet satisfactory, for a large percentage of the genes. Consistency checks are needed, which may then suggest re-annotation, and in some cases resequencing or imputing of unidentified/missing nucleotides in order to reveal the true gene structure. Two very recent advances make this an opportune moment to fill the remaining knowledge gap in a systematic way. The first is that in some parts of the fungal tree, there is already a high phylogenetic density of fully sequenced, annotated genomes, allowing alignment of genes and imputation with high confidence. The second is that affordable Illumina next-generation sequencing (NGS), delivering paired short reads, has now increased its read lengths to above 100 bp as well as the quality of the reads (i.e., ease of NGS-only assembly and accuracy) and the throughput one can expect at a reasonable cost. We propose to construct a sustainable, expandable, human-curatable and easily modifiable prototype database system to hold fungal gene sets (alignments of orthologous or homologous coding sequences) for the nuclear and mitochondrial protein-coding genes of species sequenced by our group and by other sequencing centers. For the prototype we will construct and test by ongoing use in this project, we propose to populate the database with the human pathogenic and other fungi of the Onygenales order, which includes important (primary) pathogens endemic in South and/or North America such as the dimorphic fungi Histoplasma capsulatum, Coccidioides spp., Paracoccidioides brasiliensis, and Blastomyces dermatitidis; as an 'outgroup' we will also include another clinically important group within the ascomycetes, such as the genus Aspergillus. The protein-coding gene sets of these taxa will be carefully corrected and curated, by imputing unidentified/missing nucleotides via alignment and re-annotation where this is possible, and by sequencing 10 previously sequenced or unsequenced strains where the initial results indicate a need for higher sequence quality, or for complementing with additional species/strains in regions of the fungal tree. We will also use this work to bring the gene sets and approximately 10,000 expected alignments to the level of a gene atlas: for the selected (and later for additional) human pathogenic fungi, we will have curated descriptions of the roles of the genes (orthology classes) and associated metadata on them. The design, platform and database structure of the system will be consciously chosen to allow, as far as possible, efficient ongoing human curation that can be sustained also after the end of the 3 year duration of the project.	spa
dc.format.extent	34 páginas.	spa
dc.identifier.instname	Colciencias	spa
dc.identifier.reponame	Repositorio Colciencias	spa
dc.identifier.repourl	http://colciencias.metabiblioteca.com.co	spa
dc.identifier.uri	https://colciencias.metadirectorio.org/handle/11146/39122
dc.language.iso	spa	spa
dc.relation.ispartofseries	Informe;
dc.rights.accessrights	info:eu-repo/semantics/openAccess	spa
dc.rights.accessrights	http://purl.org/coar/access_right/c_abf2	spa
dc.rights.accessrights	info:eu-repo/semantics/openAccess	spa
dc.rights.accessrights	http://purl.org/coar/access_right/c_abf2	spa
dc.rights.creativecommons	https://creativecommons.org/licenses/by/4.0/	spa
dc.subject.proposal	Bioinformatics	spa
dc.subject.proposal	Fungal pathogens	spa
dc.subject.proposal	Genome informatics	spa
dc.subject.proposal	Microbial genomics	spa
dc.subject.proposal	Onygenales	spa
dc.title	A gene atlas for human pathogenic fungi.	spa
dc.type	Informe de investigación	spa
dc.type.coar	http://purl.org/coar/resource_type/c_93fc	spa
dc.type.content	Text	spa
dc.type.driver	info:eu-repo/semantics/report	spa
dc.type.redcol	https://purl.org/redcol/resource_type/PID	spa
dc.type.version	info:eu-repo/semantics/submittedVersion	spa
dc.type.version	http://purl.org/coar/version/c_71e4c1898caa6e32	spa
dc.type.version	info:eu-repo/semantics/submittedVersion	spa
dc.type.version	http://purl.org/coar/version/c_71e4c1898caa6e32	spa
dcterms.audience	Estudiantes, Profesores, Comunidad científica colombiana, etc.	spa
dspace.entity.type	Publication
oaire.awardnumber	122256934875	spa
oaire.funderidentifier.colciencias	40-2013
oaire.fundername	Departamento Administrativo de Ciencia, Tecnología e Innovación [CO] Colciencias	spa
oaire.fundingstream	Programa Nacional en Ciencias Básicas	spa
oaire.objetives	To provide the biomedical and biological research communities with a sustainable database and system for fungal genes (prototype 'gene atlas'), built around a core of consistently and effectively structured, annotated, relationally linked and human curated protein-coding gene/protein alignments of human pathogenic fungi from the order Onygenales as well as from another ascomycete taxon such as Aspergillus, that can later be extended to include further human pathogenic fungi.	spa