Transcript Saccharomyces exiguus

Saccharomyces exiguus
Has S. exiguus retained
more genes from the
whole genome duplication
than S. cerevisiae?
Background information:
Background Information
1. S. exiguus is the yeast found in sourdough bread
and is part of the duo of microorganisms that give it
a distinct flavor.
2. S. exiguus does not metabolize malt sugar, allowing
for symbiotic growth with the maltose-metabolizing
bacteria Lactobacillus san francisco.
3. It is known that S. exiguus has more raw genetic
material than S. cerevisiae.
4. The two species diverged after
the duplication, but not long after.
http://editore.slowfood.com/editore/riviste/slow/EN/34/sourdoughs.htm
Question:
Because S. exiguus has more genetic
material, is this material
1. composed of functional genes
retained from the duplication,
2. retained “junk” DNA ,
3. or is the material due to subsequent
events?
Methods
Gather all known sequences of S. exiguus
DNA
Make as complete a sequence as possible
Compare to S. cerevisiae for possible hits
Determine whether these hits can be
explained through retention after the
duplication
Currently
* To determine if duplication has taken place, we
are looking on known duplication blocks to see
if additional nearby genes are on E. exiguus
* We are using the Ken
Wolfe site, comparing
the known duplicated
blocks to E. exiguus
* Only if genes are known and near can we
compare rearrangements and rule out
discontinuities
So far we have learned
65 segments of S. exiguus have been found
which correspond with two or more regions of
S. cerevisiae
Some regions have been discarded
Ribosomal DNA
Non-duplicated regions – cannot compare
A small handful of hits seem to be from duplicated
regions, possibly showing that S. exiguus has
retained additional genes
Credits - Images
Background http://botit.botany.wisc.edu/toms_fungi/dec2002.html
Budding yeast (1) –
http://library.thinkquest.org/C004535/media/s_cerevisiae.gif
Phylogenic tree http://genome.wustl.edu/genome/yeast/map.htm;
Sourdough bread http://www.recipetips.com/kitchen-tips/t--1125/breads-using-starters.asp
DNA –
http://www.dnamnd.med.usyd.edu.au/
Screenshot http://www.gen.tcd.ie/cgi-bin/khwolfe/gene.pl?name=SSB1&junk=no
Magnifying glass http://blog.labnotes.org/2006/05/31/pr-tools-and-bag-of-tricks/
To determine if duplication – on known duplication blocks
Compare to known Ken Wolfe site – for known blocks
70% of genome on a duplication block
Only if genes are known and near can we compare
rearrangements – rule out discontinuities
Took S exiguus reads – assembled
fasta files – (fasta tool compares sequences)
blast at protein level against cere orfs that had been translated
S.all.blastX
create a pearl script ==> Exiguus. all. Phits
consolidates blast info, gets rid of duplications
script – summary.pl
finds all with 2+ hits
discard
go to Wolfe site