Yeast genome sequencing is a fast-moving field of yeast research and is yielding significant results. This Thematic Issue from FEMS Yeast Research highlights the current advances being made in genome analysis and represents the progress that has been achieved over the last 25 years. Papers in this issue cover topics including fungal hybridization, RNA-seq data analysis, mass spectrometry, beer brewing, and the natural history of the Saccharomyces genus.