Despite the extensive research the exact function many
yeast genes remains unknown. Comparisons to other fungal
genomes can add power to the genomic analysis by
providing the evolutionary context of genes. Our goal is
to compare the protein coding gene contents of fungal
genomes and relate the differences to the physiological
differences between species and taxonomic groups.
We have produced consistent Interpro annotations and
clustering of protein coding sequences of 16 sequenced
fungal genomes of which 8 are yeasts. Our computational
system is based on BioPerl scripts and BioSQL schema for
storing the sequences and annotations in a relational
database. The clustering of protein sequences is done
with Tribe-MCL graph clustering software using distances
based on Blast E-values.
We have discovered that the number of genes belonging to
protein clusters having members from all fungal species
studied is negatively correlated with genome size, i.e.
larger fungal genomes are likely to have more specialized
functions not present in species with smaller genomes. In
contrast, based on protein clustering Pezizomycotina and
Saccharomycotina seem to differ in their level of
paralogy, i.e. in number of duplicated genes. In
Saccharomycotina average level of paralogy is positively
correlated to the size of the genome. In Pezizomycotina,
possibly due to Repeat Induced Point mutations (RIP), no
clear correlation exists.
Using Generic Genome Browser we have created a web-based
system that allows the scientists at VTT to easily
utilize comparative information in their work. In
particular, we link the Interpro entries and clusters so
that a user can for a particular protein family browse
the neighborhood of the family members detected by
Interpro to assess the true extend of the family. In
addition, a user can easily find the clusters and
Interpro entries that have interesting species
distributions. We also link the S. cerevisiae metabolic
model iND750 to the comparative data.
|Conference||International Specialised Symposium on Yeasts, ISSY 25 |
|Abbreviated title||ISSY 25|
|Period||18/06/06 → 21/06/06|