Saccharomyces exiguus

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Saccharomyces exiguus

• Has S. exiguus retained
• more genes from the
• whole genome duplication
• than S. cerevisiae?

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Background information
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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/E
N/34/sourdoughs.html
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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?
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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

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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

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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

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Credits - Images
Background - http//botit.botany.wisc.edu/to
ms_fungi/dec2002.html Budding yeast (1)
http//library.thinkquest.org/C004535/media/s_cere
visiae.gif Phylogenic tree -
http//genome.wustl.edu/genome/yeast/map.htm Sou
rdough bread - http//www.recipetips.com/
kitchen-tips/t--1125/breads-using-starters.asp DN
A http//www.dnamnd.med.usyd.edu.au/
Screenshot - http//www.gen.tcd.ie/cgi-bin/
khwolfe/gene.pl?nameSSB1junkno
Magnifying glass - http//blog.labnotes.org
/2006/05/31/pr-tools-and-bag-of-tricks/
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• 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 gt Exiguus. all. Phits
• consolidates blast info, gets rid of duplications
• script summary.pl
• finds all with 2 hits
• discard
• go to Wolfe site