CAREER: The de novo discovery of transposable elements for the study of neutral substitution rate variation in plant genomes

Miami University, Oxford OH

Investigators

Abstract

Miami University (Ohio) is awarded a grant from the Faculty Early Career Development program (CAREER) for the development of algorithms related to the automatic annotation of transposable elements, as well as the analysis of the results to expand our understanding of the roll of neutral substitution rates and other processes in the evolutionary history of animal and plant genomes. Transposable elements are pervasive across the genomes of higher order organisms and are a fundamental force behind genomic evolution. They are also are one of the key data sources for studying evolutionary processes at the genomic level. But while effective algorithmic methods exist for the identification of transposable elements that have retained sufficient sequence similarity to their progenitor, the capability of these methods quickly diminishes when searching for transposable elements that have experienced a higher level of sequence decay due to age or presence in more evolutionary volatile genomic regions. The key research results of this study will include 1) the mathematical formulation and implementation of an algorithm underlying a comprehensive de novo generation of transposable element libraries, 2) a fast, sensitive search tool for transposable elements based on that library, 3) a model of transposable element domain structure leading to the improvement of transposable element discovery, 4) an improved understanding of mammalian neutral substitution rates from a transposable element based analysis, and 5) adaptation of the same methodology of neutral substitution rate analysis to plant genomes and a comprehensive study of rate variation in plants. This grant will also provide an opportunity to develop aspects of a comprehensive bioinformatics program using the proposed research as the background for the introduction of new students into the field. In addition to using the problem of transposable element annotation as the basis for an introductory programming class targeted towards undergraduate biologists, an online Bioinformatics course will be developed and implemented with the goal of allowing the remote teaching of the subject at schools without the resources to maintain their own program. To this end, we will specifically target Berea College, an institution exclusively serving economically disadvantaged students, developing a bioinformatics module to be incorporated into certain courses and an annual workshop designed to expose their students to the field. For more information see the project website at http://www.eas.muohio.edu/people/karroje.