title: Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.
abstract: As manually curated and non-automated BLAST analysis of the published Pichia pastoris genome sequences revealed many differences between the gene annotations of the strains GS115 and CBS7435, RNA-Seq analysis, supported by proteomics, was performed to improve the genome annotation. Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to all P. pastoris sequences. This allowed the identification of 492 new ORFs, 4916 hypothetical UTRs and the correction of 341 incorrect ORF predictions, which were mainly due to the presence of upstream ATG or erroneous intron predictions. Moreover, 175 previously erroneously annotated ORFs need to be removed from the annotation. In total, we have annotated 5325 ORFs. Regarding the functionality of those genes, we improved all gene and protein descriptions. Thereby, the percentage of ORFs with functional annotation was increased from 48% to 73%. Furthermore, we defined functional groups, covering 25 biological cellular processes of interest, by grouping all genes that are part of the defined process. All data are presented in the newly launched genome browser and database available at www.pichiagenome.org In summary, we present a wide spectrum of curation of the P. pastoris genome annotation from gene level to protein function.
authors.affiliation: Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria.
authors.forename: Minoska
authors.initials: M
authors.lastname: Valli
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH-Campus, 1190 Vienna, Austria.
authors.forename: Nadine E
authors.initials: NE
authors.lastname: Tatto
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH-Campus, 1190 Vienna, Austria.
authors.forename: Armin
authors.initials: A
authors.lastname: Peymann
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria Department of Chemistry, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
authors.forename: Clemens
authors.initials: C
authors.lastname: Gruber
authors.affiliation: Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria.
authors.forename: Nils
authors.initials: N
authors.lastname: Landes
authors.affiliation: The Vienna Biocenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria.
authors.forename: Heinz
authors.initials: H
authors.lastname: Ekker
authors.affiliation: Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria.
authors.forename: Gerhard G
authors.initials: GG
authors.lastname: Thallinger
authors.affiliation: Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria.
authors.forename: Diethard
authors.initials: D
authors.lastname: Mattanovich
authors.affiliation: Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria brigitte.gasser@boku.ac.at.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Gasser
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH-Campus, 1190 Vienna, Austria.
authors.forename: Alexandra B
authors.initials: AB
authors.lastname: Graf
mesh_terms: D019295:Computational Biology; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism*; D005800:Genes, Fungal; D058977:Molecular Sequence Annotation; D010843:Pichia / Q000235:genetics* / Q000502:physiology*
chemical_list: D005656:Fungal Proteins
keywords: RNA-Seq; functional annotation; genome sequence; methylotrophic yeast; protein domains; proteomics