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Background   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 . 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.    Results  We 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.    Conclusions  We 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.

Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris)