Alice Hu
Faculty Advisor: Lukas Mueller
Year: 2018

“Analysis of Iochroma cyaneum Gene Families”

Project Summary:

Gene duplication and loss is an important force driving the evolution of species. The resulting gene families are an essential aspect to understanding functional differences between species. We looked at the Iochroma cyaneum genome, which had not yet been well characterized, and compared it to other plant species (the genomes of Arabidopsis thaliana , cultivated tomato, coffee, a wild relative of tomato , potato, eggplant , pepper , Petunia axillaris, morning glory, grape, and rice) to clarify its position on the phylogenetic tree and identify gene families that seem to be rapidly evolving. With the assistance of multiple computer programs, we were able to incorporate the genes from the listed species into gene family analysis. I. cyaneum is an important species, since it has been used to study the evolution of floral morphology and pigment in addition to containing various phytochemicals having potential pharmaceutical uses. Using BUSCO (Benchmarking Universal Single-Copy Orthologs), we assessed the completeness of the I. cyaneum genome and annotation, and displayed the results in a genome and a protein barchart. The results of the OrthoFinder program were compared to previous results from an older program, OrthoMCL, to detect contractions and expansions of Iochroma gene families and assess differences in gene family detection between the two software packages. We ran KinFin on the Orthofinder results to associate representative functions to orthogroups, and RAxML to generate the phylogenetic tree. The tree showed that Iochroma was most closely related to pepper.

My Experience:

My experience at BTI this summer has been exciting and informative. Before this internship, I had never worked in a research environment or a professional setting. Throughout these past six weeks, I’ve gained a new interest in bioinformatics and computer science and learned to use the resources I have to my advantage. I would like to thank my mentor, Suzy Strickler, for guiding me through my research and exposing me to the world of scientific research. I am very thankful for this incredible opportunity to participate in this internship.