Work Address:
University of California
Department of Plant and Microbial Biology
111 Koshland Hall # 3102
Berkeley, California 94720-3102
321 Koshland Hall lab phone: 510.642.8441
fax: 510.642.4995
email: jason_stajich [at] berkeley.edu
CV (PDF)
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Work Address: |
Jason joined the Taylor lab in August of 2006 after completing his PhD on "Comparative analysis of fungal genome evolution" at Duke University in May 2006. During my time at Duke I built a website for interacting with fungal genomes to display data from my thesis work. We are working to build another site to provide comparative genomic data, automated genome annotation, and phylogenies. The site also includes a blog about comparative genomics where we are keeping track of recent news and publications related to the study of fungal genomes.I am interested in the evolution and adaption of fungi. I use comparative genomics, molecular evolution, phylogenetic tools to study gene and genome evolution. My current projects focus on comparisons among closely related fungi and on patterns of change across the entire kingdom of fungi.
Comparison of closely related animal pathogenic and non-pathogenic fungi
I have projects focusing on genomes of closely related species include the human pathogenic fungi Coccidioides immitis and C. posadasii. We are applying comparative genomics and transcriptional profiling to study the evolution of these pathogens as well as their pathogenic and non-pathogenic relatives in the Onygenales such as Uncinocarpus, Histoplasma, and Blastomyces. With additional whole genome sequencing of from different populations we also approaching the question of evolution of pathogenecity from a population genomics perspective.In the Taylor lab, we are also interested in the evolution of Neurospora crassa and related species N. tetrasperma and N. discreta. We are involved in the JGI's genome sequencing of N. tetrasperma and N. discreta to address questions about evolution of sex determining regions. We are also using comparative genomics to predict and validate novel genes in N. crassa.
Evolution of development and multicellularity in fungi
I am also studying the genome of the amphibian killing chytrid fungus, Batrachochytium dendrobatidis in collaboration with sequencing groups JGI and Broad Institute. Chytrids are water molds which have motile zoospores with flagella enabling them to swim. Previous work has shown that the flagella was lost after Chytrid lineage diverged from the lineage leading to the rest of the fungi. Comparisons of this fungus to animal genomes and members of the fungal kingdom will help us learn what genes and processes were present in the fungal-animal ancestor (or Opisthokont) and the transitions to other major groups of fungi including those with multicellular forms. The B. dendrobatidis work is also a collaboration with Erica Rosenblum (Eisen lab) on work exploring the gene expression changes in B. dendrobatidis during life stages and infection of frogs.
Working with collaborators I am exploring the evolution of the Basidiomycete mushroom Coprinus cinereus (Coprinopsis cinerea) using comparative genomics. We are focusing on evolutionary transitions in the Homobasidiomycetes as well as transcriptional and functional aspects of mushroom development. This work along with comparisons of unicellular and multicellular fungi will build a better understanding of the evolution of development and how multicellularity arose in the Fungi.New tools for comparative genomics and bioinformatics
I participate in the development of reusable tools for bioinformatics and comparative genomic analyses. I helped lead and develop the BioPerl toolkit that provides resuable Perl modules for processing bioinformatics data and reports. I am most interested in new tools for enabling phyloinformatics (phylogenetic data management and pipeling), phylogenomics (phylogenetic inference applied to datasets of whole genomes), and population genomics (population genetics applied to datasets of whole genomes).Within the Fungi we are lucky to have 70+ whole genome datasets as well as multiple genome re-sequencing of several strains where automated multi-locus phylogenetic and population genetic studies can be applied to better understand the history of selective pressures and adaptations among diverse and fascinating fungal species.