ABI Innovation: New Software Tools for Genome Comparisons of Non-Model Organisms

Carnegie Mellon University, Pittsburgh PA

Investigators

Abstract

Recent advances in high-throughput sequencing technologies have allowed study of the genomes of many more non-model organisms. The comparisons of these genomes will provide new insights into the evolution of complex traits of different species. This project will develop new methods to compare more than ten new bee genomes to help elucidate the molecular signatures of eusociality using evolutionary genomics. Eusocial species have different levels of social organization while related species are solitary, providing an ideal "ladder" of species to study the evolution of social life. The genetic basis for such phenotypes has remained largely unexplored until very recently. In this research, new tools will be developed to better annotate the gene models by incorporating both RNA-seq data and information from genome sequences of related organisms. The method will fully utilize splice variants when annotating the gene models. Methods will also be developed to build high-quality cross-species sequence alignments for both coding and non-coding regions in the bee genomes. Additionally, errors in the original genome assemblies will be corrected to improve quality. Insights from this project can be applied to other species and clades as the data becomes available. This research involves interactions between computational and experimental biologists. The project will develop computational biology curricula and train graduate students in interdisciplinary research methods. The research developed in this project will be integrated into existing outreach programs (such as the G.A.M.E.S. camp and the SING workshop at the University of Illinois) to encourage undergraduate students to pursue careers in science and engineering. The tools and data produced in the project will be made available through a project website.