Filip Jander
Year: 2016
Faculty Advisor: Lukas Mueller

Solanaceae Gene Family Analysis


Project Summary

This project consisted of analyzing the newly sequenced Iochroma cyaneum genome and comparing it to Solanum lycopersicum (tomato), Solanum tuberosum (potato) and Arabidopsis thaliana. The purpose of the project was to identify gene families and provide the groundwork for interesting/unique genes and gene families in Iochroma and the Solanaceae. I ran scripts on the servers to generate data that was used to create a Venn diagram to show the gene family relationships. The research was successful, as the data that we got was expected because Arabidopsis thaliana didn’t have as many gene families in common as tomato, potato and Iochroma. A large number of singletons were found in the Iochroma annotations, likely due to the lower quality of the gene structural annotations. However, overall the Iochroma gene annotations were of acceptable quality.

The second part of the project involved creating a phylogeny tree to develop a better understanding of how Iochroma cyaneum evolved from the rest of the Solanaceae family. For this part of the project I worked with various programs to analyze eight species in the Solanaceae family. The result of this portion of the project was the completed phylogeny tree of the eight species using a dataset of ortholougs genes. This phylogeny is based on a larger number of data than previous phylogenies for these species. The Iochroma cyaneum genome is most likely the largest source of error in this project because of the inaccuracies of draft genome assemblies and annotations.

My Experience

I learned a lot about unix operating systems and how they are useful for large data sets and bioinformatics. This was a great learning opportunity for me because it will help me in the future if I ever want to go into computer science. Additionally, I learned some Perl which can help me in the future if I ever choose to take on bioinformatics as a profession. Working a 9-5 job taught me a lot about time management and what it’s like to be in a real work setting. Collaborating with my mentors was also a good experience for me because it helped me understand my research to get a good idea of what I was doing. Overall this internship taught me a lot and has made me consider a future in scientific research.