||The rapid development of large-scale genomic sequencing has dramatically changed the
field of genetics, in part through the development of comparative genomics. Fungal
comparative genomics is particularly powerful given the large number of genomes currently
available, their compact architecture, and their relative ease of genetic manipulation.
Fungal comparative genomics was employed in this work to address two related questions.
First, it was used along with computational thermodynamic methods to predict non-coding
RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes
were evaluated to determine the effect of window sizes and step sizes on the sensitivity
of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome
6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of
cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions.
Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural
elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding
genes were also identified. This work shows that thermodynamic approaches, coupled
with comparative genomics, are powerful tools for predicting structural ncRNA.
Second, comparative genomic approaches were employed to identify a non-reciprocal
transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million
years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental
var. neoformans strains from around the world contain this sequence obtained from
var. grubii. The introgression event likely occurred via an incomplete inter-varietal
sexual cycle creating a hybrid intermediate where mobile elements common to both lineages
mediated the exchange. The subsequent duplication in laboratory strains of a fragment
of this same genomic region supports evolutionary theories that instabilities in subtelomeric
regions promote adaptive evolution through gene amplification and subsequent adaptation.
These data indicate that DNA exchange between closely related sympatric varieties
or species may be a recurrent theme in the evolution of fungal species. It further
suggests that while evolutionary divergence is the primary force driving speciation,
rare introgression events also play a potentially important role.