Book of Abstracts (PDF) - International Mycological Association

IMC7 Thursday August 15th Lectures
regions were identified (Fischer et al., 2001, Genome Res,
11, 2009-2019). These traces were called relics rather than
pseudogenes because of the high number of mutations
accumulated in these sequences that erased all
characteristics of an ORF. A genome-wide search for relics
in S. cerevisiae reveals the presence of at least 130
intergenic regions showing weak homology to functional
ORFs. The combined chromosomal localization of the
relics, the members of the multigene families and the transchromosomal
series identified during the Génolevures
program reveal some overlap between the different
duplicated regions showing that at least part of the
redundancy in the yeast genome results from a dynamic
equilibrium between gene duplications and gene losses.
335 - Comparison of genomic data of the cotton
pathogenic fungus Ashbya gossypii with Saccharomyces
cerevisiae
P. Philippsen 1* , F. Dietrich 1 , S. Brachat 1 , S. Voegeli 1 , A.
Lerch 1 , K. Gates 2 & T. Gaffney 2
1 Institute of Applied Microbiology, Biozentrum, University
of Basel, Klingelbergstrasse 50/70, CH-4056 Basel,
Switzerland. - 2 Syngenta, 3054 Cornwallis Road Reaserch
Triangle Park, NC 27709, U.S.A.
Ashbya gossypii and Saccharomyces cerevisiae are very
different ascomycetes with respect to growth form and
habitat but their genomes share remarkable similarities.
The comparison at the nearly complete map of the 4800 A.
gossypii ORFs with the map of the 6200 S. cerevisiae
ORFs reveals the following results: 1. For 96% of the A.
gossypii ORFs homologs are found in S. cerevisiae. 2. The
majority of these homologs are present in S. cerevisiae as
duplicated segments with up to 50 genes displaying relaxed
synteny with the A. gossypii gene order. 3. Most duplicated
S. cerevisiae ORFs are present as single copy ORFs in A.
gossypii, e.g. RAS1/RAS2, TOR1/TOR2, MYO2/MYO4,
CLB1/CLB2 and many others. Several of these 'ancient
twin ORFs' code for functionally different proteins in S.
cerevisiae and it is an open question which function is
encoded by the single A. gossypii ORF. 4. At least 300
functional S. cerevisiae ORFs are not present, or no longer
present in A. gossypii. 5. Homologs for several of the S.
cerevisiae ORFs annotated as questionable were detected at
syntenic positions in A. gossypii. However for most of
these ORFs no homolog was found in A. gossypii. 6. The A.
gossypii genome contains many gene families, which are
also, present in the S. cerevisiae genome, but often with
fewer members. Implications of these results with respect
to the evolution of both genomes will be discussed.
336 - Evolution of the yeast genome
J. Piskur
Section for Molecular Biology, BioCentrum-DTU,
Technical University of Denmark, Building 301, DK-2800
Lyngby, Denmark. - E-mail: imjp@pop.dtu.dk
106
Book of Abstracts
The genetic material has often been rearranged during the
evolutionary history of various organisms. For example,
gene duplications and rearrangements of the gene order
have been particularly frequent. The most plausible way to
deduce the molecular mechanisms, which are responsible
for these changes, is to compare the genomes of closely
related contemporary species. Because yeast species are
easy to manipulate in the laboratory and the yeast genomes
are relatively small, these organisms represent ideal models
to understand the molecular evolution of eukaryotic
genomes. In collaboration with laboratories from France
and U.S., several Saccharomyces species were recently
analysed for the structure of their mitochondrial and
nuclear genomes. Several mitochondrial DNA molecules
were mapped for their genes and a couple of the
mitochondrial genomes was recently totally sequenced to
get an idea about the origin of the present mitochondrial
gene order. A number of nuclear genes, homologous to the
duplicated S. cerevisiae genes, were analysed for their
phylogenetic relationship to deduce the timing of the
duplication, as well as the gene differentiation event(s).
337 - PHOREST: a web based tool for comparative
analysis of EST data
D.G. Ahrén 1* , C. Troein 2 , T. Johansson 1 & A. Tunlid 1
1 Microbial Ecology, Lund University, Ecology Building,
223 62 Lund, Sweden. - 2 Theoretical Physics, Complex
systems, Lund University, Sölvegatan 14 A, 223 62 Lund,
Sweden. - E-mail: dag.ahren@mbioekol.lu.se
Large-scale sequencing of cDNAs prepared from specific
tissue or material prepared under different growth
conditions has proven to be an efficient way for gene
discovery. For such applications, we present PHOREST, a
web-based tool for managing, analyzing and comparing
various collections of expressed sequence tags (ESTs).
PHOREST is specifically designed to support EST data
projects and for successively receiving and incorporating
data as project grows. After entry of sequence data a search
for homologous sequence information in publicly available
databases is automatically conducted, followed by
assembly of ESTs/clones into contigs. After manual
annotation of contigs the redundancy and distribution of
transcripts/contigs into functional categories can be
analyzed. Several projects/databases can be managed in
parallel and overall assembly and normalization of data
display transcripts/contigs being differentially regulated in
the different projects can be compared. Access can be set
for multiple users to search and annotate the same dataset
without interference. The tool has been used for two EST
projects comparing three different stages of fungal growth
and infection. The projects are comparing stages in a
nematode-trapping fungus, Monacrosporium haptotylum
and a mycorrhizal fungus, Paxillus involutus.