David Lyon
David Lyon
Year: 2016
Faculty Advisor: Lukas Mueller

Identification of Conserved Noncoding Sequences in Papilionoid Legumes and their Impact on the Evolution of Nodulation

Project Summary

Conserved noncoding sequences (CNSs) are regions of DNA that are evolutionarily conserved but not translated. These regions have been shown to have an effect on expression dynamics. Studying and mining CNSs may be a good way to elucidate the evolutionary mechanisms that underlie important developmental processes. Previously, a pipeline was developed to create multi-genome alignments of conserved regions using LASTZ and PhastCons . The current project is focused on analyzing the output from that pipeline. Specifically, it focuses on the aligned genomes of 11 species from the legume family, all from the papilionoid subfamily, which is composed of around 700 genera and 14,000 species, and includes nearly all of the economically important and model legumes.

To assist identifying and characterizing CNSs related to expression of genes involved in various processes, particularly root nodulation, a program called CNSTools was developed. CNSTools analyzes masked multi-alignment files (.maf), along with conservation scores and genome annotation files. It then outputs CNSs, their likely associations to nearby genes, and their locations on each genome. CNSTools identified many CNSs between the input genomes within the legume dataset. These sequences were then scanned for motifs and checked for associations to genes known to be related to nodulation. It is hoped that these results, and the software developed in order to obtain them, can help to create a deeper understanding both of nodulation and the role of CNSs as a whole.

My Experience

My internship at Boyce Thompson Institute helped me to solidify my desire to pursue a graduate degree, and eventually a career, in bioinformatics in the future. During my time there, I learned new computational techniques for processing biological data and was given both the freedom and support to explore my research through literature and hands-on research. I also gained experience in working within a research lab as my previous research experience exclusively came from working in small independent labs. Overall I strongly believe that my time at BTI was not only a wonderful experience, but one which I will find myself being extremely grateful for as I continue research in bioinformatics.