Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex

Abstract

The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the Ogataea polymorpha species complex, including representatives of the species O. polymorpha, O. parapolymorpha, O. haglerorum, and O. angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.

Nuclear genome organization in fungi: from gene folding to Rabl chromosomes

“…In addition to the critical link between gene expression and chromatin folding, several conserved DNA-templated processes may be directly tied to genome organization, including DNA replication and repair that can alter genome and nuclear organization. DNA repair events can contribute to fungal evolution, as the occurrence of a double stranded DNA break and its concomitant repair onto DNA strands spatially close in 3D may be the first step in structurally varying a species’ genome (Zhang et al 2012 , Hanson et al 2021 , Huang and Cook 2022 ). Thus, DNA-templated processes in the nucleus are often influenced by the organization of the genome, yet improper functioning of these genomic functions can feedback and alter genome organization, highlighting the intricate interconnection between chromosome conformations and genome function.…”