title: The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.
abstract: The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community. In addition to being a repository and central point of access to genome, transcriptome and polymorphism data, AspGD hosts a comprehensive comparative genomics toolbox that facilitates the exploration of precomputed orthologs among the 20 currently available Aspergillus genomes. AspGD curators perform gene product annotation based on review of the literature for four key Aspergillus species: Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus and Aspergillus niger. We have iteratively improved the structural annotation of Aspergillus genomes through the analysis of publicly available transcription data, mostly expressed sequenced tags, as described in a previous NAR Database article (Arnaud et al. 2012). In this update, we report substantive structural annotation improvements for A. nidulans, A. oryzae and A. fumigatus genomes based on recently available RNA-Seq data. Over 26 000 loci were updated across these species; although those primarily comprise the addition and extension of untranslated regions (UTRs), the new analysis also enabled over 1000 modifications affecting the coding sequence of genes in each target genome.
authors.affiliation: Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02141, USA Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
authors.forename: Gustavo C
authors.initials: GC
authors.lastname: Cerqueira
authors.forename: Martha B
authors.initials: MB
authors.lastname: Arnaud
authors.forename: Diane O
authors.initials: DO
authors.lastname: Inglis
authors.forename: Marek S
authors.initials: MS
authors.lastname: Skrzypek
authors.forename: Gail
authors.initials: G
authors.lastname: Binkley
authors.forename: Matt
authors.initials: M
authors.lastname: Simison
authors.forename: Stuart R
authors.initials: SR
authors.lastname: Miyasato
authors.forename: Jonathan
authors.initials: J
authors.lastname: Binkley
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Prachi
authors.initials: P
authors.lastname: Shah
authors.forename: Farrell
authors.initials: F
authors.lastname: Wymore
authors.forename: Gavin
authors.initials: G
authors.lastname: Sherlock
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
mesh_terms: D001230:Aspergillus / Q000235:genetics*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D020407:Internet; D058977:Molecular Sequence Annotation; D017423:Sequence Analysis, RNA