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FEMS Yeast Res. 2016 Sep;16(6). pii: fow051. doi: 10.1093/femsyr/fow051. Epub 2016 Jul 6.

Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.

Author information

1
Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria.
2
Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH-Campus, 1190 Vienna, Austria.
3
Austrian Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria Department of Chemistry, BOKU University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
4
The Vienna Biocenter Core Facilities GmbH (VBCF), 1030 Vienna, Austria.
5
Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria.
6
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.

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.

KEYWORDS:

RNA-Seq; functional annotation; genome sequence; methylotrophic yeast; protein domains; proteomics

PMID:
27388471
DOI:
10.1093/femsyr/fow051
[Indexed for MEDLINE]
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