The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic

Abstract

Microorganisms need to adapt to environmental changes, and genome plasticity can lead to rapid adaptation to hostile environments by increasing genetic diversity. Here, we investigate genome plasticity in the CTG(Ser1) yeast Scheffersomyces stipitis, an organism with an enormous potential for second-generation biofuel production. We demonstrate that S. stipitis has an intrinsically plastic genome and that different S. stipitis isolates have genomes with distinct chromosome organisation. Real-time evolution experiments show that S. stipitis genome plasticity is common and rapid as extensive genomic changes with fitness benefits are detected following in vitro evolution experiments. Hybrid MinION Nanopore and Illumina genome sequencing identifies retrotransposons as major drivers of genome diversity. Indeed, the number and position of retrotransposons is different in different S. stipitis isolates, and retrotransposon-rich regions of the genome are sites of chromosome rearrangements. Our findings provide important insights into the adaptation strategies of the CTG (Ser1) yeast clade and have critical implications in the development of second-generation biofuels. These data highlight that genome plasticity is an essential factor to be considered for the development of sustainable S. stipitis platforms for second-generation biofuels production.