EAGER: Variant Graph-based Genome Annotation and Analyses for Plant Genomes

University Of Utah, Salt Lake City UT

Investigators

Abstract

Advances in next-generation sequencing have opened up additional avenues of investigation due to the reduction in costs and the bioinformatic tools and functional resources available. That said, there is still a critical need for advancing sequence visualization tools to aid in sequence analysis. This EAGER project will develop a new type of genome representation - a Variant Graph which provides an innovative way to visualize and identify variants in genome sequences across related populations within a species. If successfully implemented, a Variant Graph will provide a novel means to leverage next generation sequencing data to create more accurate gene models. In addition, a fully Variant Graph based MAKER-P genome annotation pipeline will provide a leap forwards in genome-annotation and project management by providing a means for simultaneously annotating and managing genome sequences generated from multiple plant cultivars through Gramene (www.gramene.org) and CyVerse (formerly the iPlant Collaborative; www.cyverse.org). The goals of this project are to take advantage of the wealth of sequence assemblies available for plants to (1) create and deploy a Variant Graph for crop plants using genome sequences available for maize and rice through the Gramene database; (2) leverage MAKER-P to create the first genome-annotation pipeline capable of exploiting the full potential of the Variant Graph to improve the annotations of the maize and rice reference assemblies; and, (3) deploy a cutting-edge Variant Graph based variant-calling pipeline within Gramene. The project will provide interdisciplinary research training in software development and applications for plant biology and genomics for a postdoctoral associate. All software developed as part of this project will be open source and available for academic use.