Ivana Rodriguez
Year: 2015
Faculty Advisor: Lukas Mueller

Analysis and characterization of conserved non-coding sequences in species of the Legume Family (Fabaceae)

Project Summary

A character of considerable evolutionary and ecological significance is nodulation, the symbiotic fixation of atmospheric nitrogen by soil bacteria housed in specialized structures (nodules) of various angiosperms, particularly the diverse legume family. Conserved non-coding sequences (CNSs) are regions of DNA in close proximity to genes, and they serve regulatory purposes not yet fully understood in gene function. Previous work has demonstrated the mechanisms by which gene regulation provides crucial contributions and influences evolutionary change among species. Analysis of these highly conserved sequences may provide a novel way by which to track evolutionary changes and relationships among Leguminosae species on a genomics scale. More precisely, conserved non-coding sequence have great potential to supply novel evolutionary insights and may answer the question of whether these economically crucial nitrogen-fixing species have acquired their traits through a common ancestor, or through independent (convergent) means.

This project focused on assembling a pipeline by which to streamline identification of conserved sequences using whole genome data for the legume species. The location of these sequences was determined relative to coding regions to gain insight into the classes of genes the CNSs may be regulating. The identified sequences were further characterized by defining over-represented motifs, which were then queried against databases of transcription factor binding sites to obtain putative functions. Once we can deduce CNS sequences that are associated with nodulation-specific functions, additional hypotheses concerning the origins and evolution of nodulation can be deduced. Ultimately, this bioinformatics approach will serve to complement progress towards discovering evolutionary origins of nodulation.

My Experience

My internship at Boyce Thompson helped solidify my passion for discovery and research in plant genetics and genomics. My time spent at Cornell this summer helped me fulfill new goals I never thought I’d have the confidence to reach. Prior to the internship, I had almost no experience with computational biology, but with the help of my mentors, I’ve become well-oriented with bioinformatic data analysis. I was able to reach new heights in my understanding of what it means to be a scientist, and for me, that is an exhilarating and valuable feeling. I am immensely thankful to everyone in Dr. Mueller’s lab, as well as Dr. Suzy Strickler and Dr. Doyle for their endless support, faith and patience.