An Exploration of Copy Number Variation Between the Sexes: Drosophila melanogaster

Copy number variation (CNV) is a growing field of study in genomics research.  It has become clear in recent years that CNVs have a much larger impact on evolution and disease than was previously thought. Copy number variation is classified as a significant difference in copies of a DNA sequence in comparison to other individuals of the same species. These mutations can have any kind of effect, from positive to negative. They can cause diseases, such as Down’s Syndrome, but they can also give an evolutionary advantage, as the chorion protein in fruit flies shows.

In female Drosophila melanogaster, the chorion protein is used to build the shell of the eggs for protection. The female fly needs a large amount of this protein very quickly during egg development, so the genes for the chorion protein replicate themselves in order to satisfy this need. This is a very unusual process, since most of the time, when a large amount of protein is needed, large numbers of mRNA are created and stored before creating the protein. This type of adaption could be very helpful in treating diseases caused by a lack of a protein in the body. I analyzed sex specific CNV in Drosophila melanogaster in order to determine if there were other segments of DNA that replicated in flies similar to the chorion protein, which is sex specific itself.

To study these important mutations, it is necessary to analyze very large datasets. It is difficult to identify these variations without at least a large portion of different individuals’ genomes to compare each section with. Since CNVs can be as large as entire chromosomes or as small as a few nucleotides, it is very important to have large datasets to limit the amount of background noise in an analysis. With such datasets, analysis must be done using bioinformatics in order to have any level of accuracy. There are programs available to attempt to identify CNV; however, the majority of them are used to identify much smaller CNV than what I was looking for, so I created my own method.

In this paper, I use bioinformatics to identify new copy number variants in fruit flies that are different between the sexes. I am only looking at fairly large CNVs in an attempt to identify more variants similar to the chorion protein CNV. I used a combination of my own programs and already extant programs to create an analysis workflow to identify possible sites of CNV in the flies. I identified a few possible CNVs in the male flies on the X chromosome, indicating that these could be sex specific due to the difference in how the male and female flies manage their X chromosome proteins.