Abstract
We have sequenced and annotated the genome of the filamentous ascomycete
Ashbya gossypii
. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of
A. gossypii
genes show both homology and a particular pattern of synteny with
Saccharomyces cerevisiae
. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of
S. cerevisiae
included a whole genome duplication orfusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies.