title: Refined Pichia pastoris reference genome sequence.
abstract: Strains of the species Komagataella phaffii are the most frequently used "Pichia pastoris" strains employed for recombinant protein production as well as studies on peroxisome biogenesis, autophagy and secretory pathway analyses. Genome sequencing of several different P. pastoris strains has provided the foundation for understanding these cellular functions in recent genomics, transcriptomics and proteomics experiments. This experimentation has identified mistakes, gaps and incorrectly annotated open reading frames in the previously published draft genome sequences. Here, a refined reference genome is presented, generated with genome and transcriptome sequencing data from multiple P. pastoris strains. Twelve major sequence gaps from 20 to 6000 base pairs were closed and 5111 out of 5256 putative open reading frames were manually curated and confirmed by RNA-seq and published LC-MS/MS data, including the addition of new open reading frames (ORFs) and a reduction in the number of spliced genes from 797 to 571. One chromosomal fragment of 76kbp between two previous gaps on chromosome 1 and another 134kbp fragment at the end of chromosome 4, as well as several shorter fragments needed re-orientation. In total more than 500 positions in the genome have been corrected. This reference genome is presented with new chromosomal numbering, positioning ribosomal repeats at the distal ends of the four chromosomes, and includes predicted chromosomal centromeres as well as the sequence of two linear cytoplasmic plasmids of 13.1 and 9.5kbp found in some strains of P. pastoris.
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria.
authors.forename: Lukas
authors.initials: L
authors.lastname: Sturmberger
authors.affiliation: BioGrammatics Inc., 2120 Las Palmas Drive, Carlsbad, CA 92011, United States.
authors.forename: Thomas
authors.initials: T
authors.lastname: Chappell
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria.
authors.forename: Martina
authors.initials: M
authors.lastname: Geier
authors.affiliation: Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Florian
authors.initials: F
authors.lastname: Krainer
authors.affiliation: Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th St., Chicago, IL 60637, United States.
authors.forename: Kasey J
authors.initials: KJ
authors.lastname: Day
authors.affiliation: Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Ursa
authors.initials: U
authors.lastname: Vide
authors.affiliation: Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Sara
authors.initials: S
authors.lastname: Trstenjak
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria.
authors.forename: Anja
authors.initials: A
authors.lastname: Schiefer
authors.affiliation: Synthetic Genomics, Inc., 11149 North Torrey Pines Rd., La Jolla, CA 92037, United States.
authors.forename: Toby
authors.initials: T
authors.lastname: Richardson
authors.affiliation: Synthetic Genomics, Inc., 11149 North Torrey Pines Rd., La Jolla, CA 92037, United States.
authors.forename: Leah
authors.initials: L
authors.lastname: Soriaga
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria; Institute of Pathology, Research Unit Functional Proteomics and Metabolic Pathways, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
authors.forename: Barbara
authors.initials: B
authors.lastname: Darnhofer
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria; Institute of Pathology, Research Unit Functional Proteomics and Metabolic Pathways, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
authors.forename: Ruth
authors.initials: R
authors.lastname: Birner-Gruenberger
authors.affiliation: Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th St., Chicago, IL 60637, United States.
authors.forename: Benjamin S
authors.initials: BS
authors.lastname: Glick
authors.affiliation: BioGrammatics Inc., 2120 Las Palmas Drive, Carlsbad, CA 92011, United States; Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, United States.
authors.forename: Ilya
authors.initials: I
authors.lastname: Tolstorukov
authors.affiliation: BioGrammatics Inc., 2120 Las Palmas Drive, Carlsbad, CA 92011, United States; Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, United States.
authors.forename: James
authors.initials: J
authors.lastname: Cregg
authors.affiliation: BioGrammatics Inc., 2120 Las Palmas Drive, Carlsbad, CA 92011, United States.
authors.forename: Knut
authors.initials: K
authors.lastname: Madden
authors.affiliation: Austrian Center of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; bisy e.U., Wetzawinkel 20, 8200 Hofstaetten/Raab, Austria. Electronic address: a.glieder@tugraz.at.
authors.forename: Anton
authors.initials: A
authors.lastname: Glieder
mesh_terms: D017398:Alternative Splicing; D002503:Centromere / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics*; D005818:Genetic Engineering; D016681:Genome, Fungal / Q000235:genetics*; D010843:Pichia / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D011993:Recombinant Fusion Proteins
keywords: Centromere; Genome; Killer plasmid; P. pastoris; RNA-seq; Splicing