Establishing a Protocol for the Detection of Gene Duplications in Drosophila melanogaster
Noe, Megan H.
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Duplication is one of the main mechanisms to introduce new genes into a genome. Once duplicated, evolutionary forces will act upon novel genes causing them to either disappear or become fixed in the population. Previous research on duplicate gene pairs in Drosophila melanogaster has focused on duplications that have already become fixed in a given population. However, examining these duplications before they become fixed provides further insight into the evolutionary forces at work on the newly duplicated genes. Microarray hybridizations are one way to locate young genes and changes in copy number, and the efficiency of this technique makes it possible to scan an entire genome. The purpose of this experiment is to determine if the duplicated regions of the D. melanogaster genome can be detected through microarray hybridization. In this preliminary project, a wild type line was scanned against a line with a known duplication region. Levels of gene hybridization for both non-duplicated and duplicated regions of the genome were then established. A histogram of the intensity fold differences shows that the duplicated and non-duplicated regions overlap at several intensity folds. Therefore, it is important to specify an intensity fold cutoff that will reduce the amount of genes that need to be verified in a polymorphic gene search. Our research concluded that duplication screens should begin at an intensity fold differences between 1.15 and 1.20, but performing additional replications might allow this number to become more precise. This protocol and duplication amplification level can be used to scan unknown regions to estimate the number of genes that remain polymorphic in the D. melanogaster genome and eventually examine the selective forces that these genes face during their fixation phase .