ReviewJournal of biotechnology2016
Refined Pichia pastoris reference genome sequence.
Review in Journal of biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 114 citations in OpenAlex.
- A Systematic Review of the Potential of Pichia pastoris (Komagataella phaffii) as an Alternative Host for Biologics Production.Molecular biotechnology · 2024Pooled it
- Yarrowia lipolytica and Komagataella phaffii (Pichia pastoris) as Hosts for Heterologous Expression of Lipases.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Genome-Wide Landscape of Position Effect Variegation inJournal of fungi (Basel, Switzerland) · 2026Article
- Pichia pastoris RNA-Sequencing and Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Pichia pastoris Genomic Resources: Accessibility, Recommendations, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Engineering small peptide secretion inFrontiers in bioengineering and biotechnology · 2026Article
- Classical Genetics of Pichia pastoris.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A chimeric rather than native secretion signal elicits stress-related transcriptional adaption during 75k γ-secalin production inFEMS microbes · 2026Article
- Decoding the Genome of the Komagataella phaffii Type Strain CBS 2612.Yeast (Chichester, England) · 2025Article
- Genetic properties of mercury‑tolerant yeast, Pichia kudriavzevii 1P4.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- A toolkit for facilitating markerless integration of expression cassettes in Komagataella phaffii via CRISPR/Cas9.Microbial cell factories · 2025Article
- Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Construction of Heterothallic Strains ofBiomolecules · 2025Article
- Identification and functional analysis of growth rate associated long non-coding RNAs inComputational and structural biotechnology journal · 2025Article
- De novo biosynthesis of β-Arbutin in Komagataella phaffii based on metabolic engineering strategies.Microbial cell factories · 2024Article
- Harnessing alkaline-pH regulatable promoters for efficient methanol-free expression of enzymes of industrial interest in Komagataella Phaffii.Microbial cell factories · 2024Article
- Comparison of CRISPR-MAD7 and CRISPR-Cas9 for Gene Disruptions inJournal of fungi (Basel, Switzerland) · 2024Article
- Safety and efficacy of a feed additive consisting of fumonisin esterase produced withEFSA journal. European Food Safety Authority · 2024Article
- A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material.Microbial cell factories · 2023Article
- Tuning Fatty Acid Profile and Yield inBioengineering (Basel, Switzerland) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 7 institutions in 2 countries.
Funding
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.