The University of Georgia has been awarded a grant to develop a set of computational tools to help researchers understand the duplication of individual genes and entire genomes of flowering plants (angiosperms). The burgeoning set of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and genome duplication, as well as the means to deduce otherwise-cryptic relationships among particular genes. Existing algorithms for genome comparisons are largely inadequate for angiosperms due to the high frequency of whole-genome duplication and persistence of many duplicated genes. The project will extend the functionality of a new approach (MCScan) for alignment within and between such genome duplication (paralog-rich genomes), incorporating elements of both gene phylogeny and gene colinearity to distinguish between orthology and paralogy. The free online availability of intra- and inter-genome alignments for angiosperms from a single resource based on uniform standards that have been empirically validated is of utmost importance to comparative genomics. The research will employ new computational approaches and sampling as much taxonomic diversity as possible to reduce the impact of lineage-specific evolutionary constraints. Products (results) will be made available to the biological sciences research community via the Plant Genome Duplication Database (PGDD), with the functionality of a pilot implementation broadened to better interface with several other relevant resources and to expedite fine-scale studies of specific genes (ortholog versus paralog detection).
Better understanding of the relationships among angiosperm (flowering plant) genes and genomes promises (1) to empower new in silico and empirical studies to advance knowledge of the central role played by genome duplication in evolution of higher eukaryotes, by providing a wealth of well-groomed data sets from an ideal taxon and based on uniform analytical standards; and (2) to clarify angiosperm evolutionary history and provide a firm foundation upon which to base translational genomics, the leveraging of hard-won structural and functional genomic information from crown botanical models to dissect specific evolutionary novelties in many additional organisms.
The project helps to educate undergraduate and graduate students and includes a teacher internship program. Teachers in this program spend time in the summer in the lab participating in research activities. Additional information about the project may be found at www.plantgenome.uga.edu.