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Comparative genomics and bioinformatic tools for studying evolution and speciation in fungi.
J. E. STAJICH (1), T. J. Poorten (2), T. Y. James (3), D. Rodriguez (4), D. Ilut (4), K. Zamudio (4), E. B. Rosenblum (5). (1) University of California-Riverside, Riverside, CA, U.S.A.; (2) University of Idaho, Moscow, ID, U.S.A.; (3) University of Michigan, Ann Arbor, MI, U.S.A.; (4) Cornell University, Ithaca, NY, U.S.A.; (5) University of California-Berkeley, Berkeley, CA,

The patterns of genome-wide variation from population genomic studies can be used to identify the basis for adaptation, dispersal range, and degree of hybridization among strains. <i>Batrachochytrium dendrobatidis</i> is a diploid chytrid fungus and an amphibian pathogen. It is currently one of the most important emerging invasive disease affecting biodiversity of frogs worldwide. Using whole genome sequencing we can extract patterns of population genomic to test the hypothesis that the fungus is cryptically sexual and undergoing recombination, or that the diploid represents an asexual lineage that undergoes a parasexual or other chromosome copy number based changes to shuffle genetic content. Further comparisons among closely related species were used to polarize changes in the genome focus on likely recent adaptations that are specific to the pathogen. Using the map of polymorphisms from genome sequencing and genotyping, comparative genomics for gene order conservation comparisons, and phylogenetic approaches, we can identify loci that adhere to and violate expectations for genome evolution and indicate targets of selection or related to rearrangements that have impacted compatibility between strains or species. Tools for bioinformatics and databases and software to enable these comparisons for enabling these studies and recently developed approaches will be demonstrated.<p><p>Keywords:

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