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Abstract
BackgroundKomagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris. However, almost all laboratory work on K. phaffii has utilized strains derived from a single natural isolate, CBS7435. There is little information about the sequence diversity of K. phaffii or the genetic properties of this species.ResultsWe sequenced the genomes of all the known isolates of K. phaffii. We made a genetic cross between derivatives of two isolates that differ at 44,000 single nucleotide polymorphism sites, and used this cross to analyze the rate and landscape of meiotic recombination. We conducted tetrad analysis by making use of the property that K. phaffii haploids do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetra-type ascus germinates.ConclusionsWe found that only four distinct natural isolates of K. phaffii exist in public yeast culture collections. The meiotic recombination rate in K. phaffii is approximately 3.5 times lower than in Saccharomyces cerevisiae, with an average of 25 crossovers per meiosis. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our work lays a foundation for future quantitative trait locus analysis in K. phaffii.
Highlights
Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris
The origin of this strain has been unclear because it was deposited in the CBS and NRRL culture collections in connection with a US patent granted to Phillips Petroleum, Braun‐Galleani et al Microb Cell Fact (2019) 18:211 but we show here that CBS7435 is identical to the type strain of K. phaffii, which was isolated from an oak tree
We found that K. phaffii has lower genetic diversity than S. cerevisiae, and that only four distinct natural isolates of this species are available in culture collections
Summary
Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris. Komagataella phaffii is the most widely used yeast species for production of heterologous proteins, such as the expression of antibody fragments for the pharmaceutical industry. K. phaffii is better known under its previous name Pichia pastoris, but the name ‘P. pastoris’ was discontinued in 2009 after it was discovered to have been used for heterogeneous strains that belong to two separate species, which were renamed K. phaffii and K. pastoris [5]. Their genomes differ by approximately 10% DNA sequence divergence and two reciprocal translocations [6]. X-33 is a derivative of GS115 in which the HIS4 gene was reverted to wildtype by site-directed mutagenesis [9]
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