Discovery of additional ancient genome duplications in yeasts

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages,^1,2 preceding adaptive radiations in vertebrates,^3,4,5 teleost fish,^6,7 and angiosperms.^8,9,10 In contrast to the many known ancient WGDs in animals,^11,12 and especially plants,^13,14,15 we are aware of evidence for only four WGDs in fungi.^16,17 The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species,^18,19 including the baker's yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery.¹⁶ Some studies have suggested that fungal lineages that experience chromosome²⁰ and genome¹⁶ duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data.^16,17 Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales.¹⁸ Our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.