Comparative genomics in the era of long-reads

Abstract

We, humans, have an ancient microscopic companion: yeasts. These microbial organisms have helped shape our evolution, our civilizations, and our sciences. The evolutionary event that enabled yeasts to produce alcohol more than 100 million years ago was followed with adaptations throughout the animal kingdom to tolerate it. Our realisation that yeast could be used to produce bread, beer, and wine quickly enabled us to fuel the high, caloric need of many civilizations. An international dispute nearly two centuries ago about the biological nature of yeast in alcohol production, ultimately led to the founding of microbiology and the various medicinal benefits from its practice. And today, yeasts are the ‘Swiss Army knives of biotechnology’, as they are often engineered to produced cheaper therapeutics and alternative energy sources.

Although an ancient companion, we have only begun to truly understand yeasts and their biotechnological capabilities, largely due to a new scientific instrument: genome sequencing technology. Analogous to an ‘algorithmic microscope’, genome sequencing technology is enabling us to generate large amounts of data about the genetic composition and diversity of yeasts. But it comes with a challenge: these (ever-growing) datasets are complex. So how do we properly analyse them? How do we consider the complex evolutionary histories encoded in the genomes of yeasts and other microbes alike? What new biology could we learn?