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Transcript
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