The genome of the CTG(Ser1) yeast Scheffersomyces stipitisis plastic

Abstract

Microorganisms need to adapt to environmental changes, and genome plasticity can lead to adaptation by increasing genetic diversity. The CTG (Ser1) clade of fungi is a diverse yeast group that can adapt remarkably well to hostile environments. Genome plasticity has emerged as a critical regulatory mechanism, in one member of the (Ser1) clade: the human fungal pathogen Candida albicans . However, in many aspects, C. albicans differs from other CTG (Ser1) members as it lacks a canonical sexual cycle and is an obligatory commensal. It is still unknown whether environmental CTG (Ser1) fungi with a canonical sexual cycle utilise genome plasticity as a strategy for adaptation. To address this question, we investigated genome plasticity in the CTG (Ser1) yeast Scheffersomyces stipitis. The non-pathogenic S. stipitis yeast does not live in the human host and has a canonical sexual cycle. We demonstrated that the S. stipitis genome is intrinsically unstable. Different natural isolates have a genome with a dissimilar chromosomal organisation, and extensive genomic changes are detected following in vitro evolution experiments. Hybrid MinION Nanopore and Illumina genome sequencing demonstrate that retrotransposons are major drivers of genome diversity and that variation in genes encoding adhesin-like proteins is linked to distinct phenotypes.