Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

Development Of Resources To Facilitate Cross-Species Comparisions

Anne Kwitek¹ , Steve Davis² , Mary Shimoyama³ , Zhiliang Hu⁴ , Cari Park⁴ , Diane Munzenmaier³ , Mindy Dwinell³ , James Reecy⁴

¹  University of Iowa, Dept. Internal Medicine and Molecular Physiology & Biophysics, Iowa City, IA

²  Bio::Neos Inc., Iowa City, IA

³  Medical College of Wisconsin, Dept of Physiology, Milwaukee, WI

⁴  4Iowa State University, Dept. of Animal Science, Ames, IA

Genetic research has been revolutionized by the mapping and sequencing of whole genomes. While most genome browsers and comparative genomics tools include conserved synteny and gene content information, there is a paucity of tools that also integrate mapped diseases or traits across species. We have developed a software tool, VCMap, to support visualizing chromosomal information across species (http://bioneos.com/VCMap/). This development involved the design and implementation of a separate front-end visualization interface, and a back-end database system. VCMap uses map coordinates of orthologs from various map sources to generate comparative maps. The tool also incorporates curated, biological annotations with an emphasis on Quantitative Trait Loci (QTL). This integrated visualization provides a unique link between not only the genomes, but also the biology across these species. The program allows a user to load a single map as a backbone onto which other maps from different species are aligned and then overlaid with annotation data, with the goal of incorporating not only QTL and disease annotations, but also SNP and expression data. To improve data annotation and analysis, a first version of the Vertebrate Trait Ontology has been developed in conjunction with RGD and MGI along with other contributors (INRA, EADGENE). The ontology is structured on a physiological systems basis, in order to standardize nomenclature and facilitate cross-species comparisons. Expert advice is currently being sought to aid in refinement and further development of the ontology. Taken together these resources will facilitate comparison of phenotypic data across species.