Masters of science in biology thesis?

i have to come up with a master's thesis for my master's of science in biology. the professor i am working with does genetics research in the ciliate tetrahymena thermophilia. he suggested examining a gene family or two. he also suggested looking at fusion genes. as far as capablities go this is a small school and we do have limited equipment. have access to reverse transcriptase pcr, real time pcr, bioinformatics stuff, etc. what are some gene families that would be interesting to look at? what type of thesis project could i derive from all of this. time frame: two years.