Comparative Genomics Tools for analysis of Six Dothideomycete Genomes

Author(s): Aerts, Andrea; Minovitsky, Simon; Cantor, Michael; Dubchak, Inna; Shabalov, Igor; Grigoriev, Igor; Ratnere, Igor | Abstract: Comparative genomics is a powerful tool for genome annotation and analysis. We recently initiated analysis of six of the Dothideomycete genomes that are publicly available: Mycosphaerella graminicola, Mycosphaerella fijiensis and Cochliobolus heterostropus C5 all sequenced and annotated at the DOE Joint Genome Institute as well as Alternaria brassicicola sequenced at the Washington University School of Medicine, Genome Sequencing Center and annotated by the Christopher Lawrence Lab at Virginia Bioinformatics Institute, Virginia Tech, Pyrenophora tritici-repentis and Stagonospora nodorum, both sequenced and annotated by the Broad Institute, MIT. We placed these genomes into a comparative framework equipped with tools to facilitate genome analysis: VISTA genome conservation curves linking genome browsers, gene cluster browser and protein links to homologs in all six genomes, side-by-side comparisons of KEGG pathways and KOG functions, and synteny viewer. JGI community annotation brought biologists behind each of these genomes together to explore common mechanisms of plant pathogenicity and host interactions.