Refined Pichia pastoris reference genome sequence

Lukas Sturmberger, Thomas Chappell, Martina Geier, Florian Krainer, Kasey J. Day, Ursa Vide, Sara Trstenjak, Anja Schiefer, Toby Richardson, Leah Soriaga, Barbara Darnhofer, Ruth Birner-Gruenberger, Benjamin S. Glick, Ilya Tolstorukov, James Cregg, Knut Madden, Anton Glieder

Publikation: Beitrag in einer FachzeitschriftReview eines Fachbereichs (Review article)ForschungBegutachtung

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 76 kbp between two previous gaps on chromosome 1 and another 134 kbp 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 9.5 kbp found in some strains of P. pastoris.

Originalspracheenglisch
Seiten (von - bis)121-131
Seitenumfang11
FachzeitschriftJournal of Biotechnology
Jahrgang235
DOIs
PublikationsstatusVeröffentlicht - 10 Okt 2016

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Pichia
Genes
Genome
Chromosomes
Open Reading Frames
Recombinant proteins
Chromosomes, Human, Pair 4
Peroxisomes
Recombinant DNA
Centromere
Chromosomes, Human, Pair 1
Secretory Pathway
Autophagy
Genomics
RNA
Transcriptome
Recombinant Proteins
Base Pairing
Proteomics
Plasmids

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    Refined Pichia pastoris reference genome sequence. / Sturmberger, Lukas; Chappell, Thomas; Geier, Martina; Krainer, Florian; Day, Kasey J.; Vide, Ursa; Trstenjak, Sara; Schiefer, Anja; Richardson, Toby; Soriaga, Leah; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glick, Benjamin S.; Tolstorukov, Ilya; Cregg, James; Madden, Knut; Glieder, Anton.

    in: Journal of Biotechnology, Jahrgang 235, 10.10.2016, S. 121-131.

    Publikation: Beitrag in einer FachzeitschriftReview eines Fachbereichs (Review article)ForschungBegutachtung

    Sturmberger, L, Chappell, T, Geier, M, Krainer, F, Day, KJ, Vide, U, Trstenjak, S, Schiefer, A, Richardson, T, Soriaga, L, Darnhofer, B, Birner-Gruenberger, R, Glick, BS, Tolstorukov, I, Cregg, J, Madden, K & Glieder, A 2016, 'Refined Pichia pastoris reference genome sequence' Journal of Biotechnology, Jg. 235, S. 121-131. https://doi.org/10.1016/j.jbiotec.2016.04.023
    Sturmberger L, Chappell T, Geier M, Krainer F, Day KJ, Vide U et al. Refined Pichia pastoris reference genome sequence. Journal of Biotechnology. 2016 Okt 10;235:121-131. https://doi.org/10.1016/j.jbiotec.2016.04.023
    Sturmberger, Lukas ; Chappell, Thomas ; Geier, Martina ; Krainer, Florian ; Day, Kasey J. ; Vide, Ursa ; Trstenjak, Sara ; Schiefer, Anja ; Richardson, Toby ; Soriaga, Leah ; Darnhofer, Barbara ; Birner-Gruenberger, Ruth ; Glick, Benjamin S. ; Tolstorukov, Ilya ; Cregg, James ; Madden, Knut ; Glieder, Anton. / Refined Pichia pastoris reference genome sequence. in: Journal of Biotechnology. 2016 ; Jahrgang 235. S. 121-131.
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    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 76{\^A} kbp between two previous gaps on chromosome 1 and another 134{\^A} kbp 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 9.5{\^A} kbp found in some strains of P. pastoris.",
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    AU - Sturmberger, Lukas

    AU - Chappell, Thomas

    AU - Geier, Martina

    AU - Krainer, Florian

    AU - Day, Kasey J.

    AU - Vide, Ursa

    AU - Trstenjak, Sara

    AU - Schiefer, Anja

    AU - Richardson, Toby

    AU - Soriaga, Leah

    AU - Darnhofer, Barbara

    AU - Birner-Gruenberger, Ruth

    AU - Glick, Benjamin S.

    AU - Tolstorukov, Ilya

    AU - Cregg, James

    AU - Madden, Knut

    AU - Glieder, Anton

    N1 - Copyright © 2016. Published by Elsevier B.V.

    PY - 2016/10/10

    Y1 - 2016/10/10

    N2 - 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 76 kbp between two previous gaps on chromosome 1 and another 134 kbp 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 9.5 kbp found in some strains of P. pastoris.

    AB - 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 76 kbp between two previous gaps on chromosome 1 and another 134 kbp 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 9.5 kbp found in some strains of P. pastoris.

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