Plant Pathology Graduate Program

Jason E. Stajich

Jason Stajich
Office: 951-827-2363
1207K Genomics Building
Office Hours: , not specified - not specified
Email: jason.stajich@ucr.edu

Jason E. Stajich

Associate Professor & Associate Bioinformaticist
Population and evolutionary genomics of fungi

Postdoc 2006-2009, UC Berkeley
Ph.D. Genetics and Genomics 2006, Duke University
B.S. Computer Science 1999, Duke University

Biography & Research Interests

Early diverging Chytrid and Zygomycete fungi

The early diverging Chytridiomycota and paraphyletic Zygomycota are groups of fungi with rich diversity of morphology and lifestyles.  I am working to connect classic work on detailed morphological studies with molecular and genomic tools studying aspects of cellular division, cell wall biosynthesis, and sexual and asexual forms.  I am interested in particular in how the cell walls differ among these fungi and evolved from aquatic to terrestrial fungi.  Some lineages evolved as mycoparasitic (e.g. Rozella), as pathogens of animals (e.g. Batrachochytrium dendrobatidis, Rhizopus oryzae), or of plants  and we use genome comparisons to identify candidate gene families and processes important to pathogen evolution.

Early diverging fungi also still share some characteristics retained in the Metazoa, that were lost subsequently in the Dikarya (Ascomycetes and Basidiomycetes) making these early diverging lineages good models for some studies of animal processes.  Some of these common traits include aspects of cellular division and the presence of a flagella. We are working to characterize additional developmental and signaling pathways that may make this group of fungi important model systems for cellular biology research.

Evolution of multicellularity in Fungi

The evolution of multicellular structures in fungi is the result of many changes in cell wall structure and growth, gene regulation, and related changes that started with a single-cell ancestor and give rise to the multitude of forms of fungi as molds, mushrooms, smuts, rusts, lichens, and yeasts.  We hope to unravel the evolutionary process in more detail exploring the lineage-specific pathways, new aspects of gene regulation and signaling, and evolutionary changes in cell wall biosynthesis and maintenance that will help delineate what is required to form multicellular structures in the extant fungi.

Fungal cell wall evolution

The cell wall defines the interface an organism's biotic and abiotic interactions with its environment.  The cell wall in Fungi evolved differently from their sister group Metazoa, which lack a cell wall, and typically contain chitin and beta-glucans.  We are interested in the set of genes that are required to synthesize, maintain, and remodel the cell wall as part of growth, response to stress, and developmental programs. We study how these genes evolved in fungi to learn when and how some innovations of cellular forms evolved and how this relates to evolutionary history of other organisms. Fungal cell wall processes are also useful targets for antifungal activities and so we are working to better describe the collection of genes that are important for cell walls using Neurospora crassa as a model system to test predictions experimentally.

Methods in comparative and evolutionary genomics

The interpretation of genome sequences to answer questions of evolution requires methods to manipulate, organize, and query the data. We are developing databases for incorporation of genome sequence, functional, and comparative data to address questions of comparative biology among fungi.

Human pathogenic fungi

A small fraction of the total known fungi are harmful to human health, but I am interested in the evolutionary pressures and changes that allowed a few (e.g. Coccidioides sp, Histoplasma capsulatum, Cryptococcus sp,Candida spRhizopus oryzae) to be successful primary or opportunistic human pathogens.  We have used comparative genomics to explore these questions (Sharpton et al, 2009) and additional work contrasting pathogenic and non-pathogenic fungi at the functional level and in understanding the ecology of their natural host reservoirs will teach us about the formation of pathogens. We are engaged in curation of literature for Cr. neoformans and Cr. gattii to associate genes with phenotypes and names.

Details about the work and joining the lab can be found on lab website


2015 Kavli Fellow, Kavli Frontiers of Science
2014 Alexopolous Prize, Mycological Society of America
Postdoctoral Research fellowship Miller Institute for Basic Research in Science, 2006-2009
NSF Graduate fellowship 2003-2006


Selected Research Articles (Full list)

Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, Pérez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ramírez L. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet. 2016;12(6):e1006108. doi: 10.1371/journal.pgen.1006108 

de Man TJB, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Suen G, Currie CR, Gerardo NM. The small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. PNAS 2016; 113(13):3567-72. doi: 10.1073/pnas.1518501113

Wang Y, Smith KM, Taylor JW, Freitag M, Stajich JE. Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. G3. 2015; pii: g3.115.017921. doi: 10.1534/g3.115.017921.

Liu P, Stajich JE. Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genet Biol. 2015;77:31-9. doi: 10.1016/j.fgb.2015.03.003 

James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. Shared signatures of parasitism and phylogenomics unite cryptomycota and microsporidia. Curr Biol. 2013 23(16):1548-53. doi: 10.1016/j.cub.2013.06.057.


Rosenblum EB, James TY, Zamudio KR, Poorten TJ, Ilut D, Rodriguez D, Eastman JM, Richards-Hrdlicka K, Joneson S, Jenkinson TS, Longcore JE, Parra Olea G, Toledo LF, Arellano ML, Medina EM, Restrepo S, Flechas SV, Berger L, Briggs CJ, Stajich JE. Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. PNAS. 2013 110(23):9385-90. doi: 10.1073/pnas.1300130110.

Robb SM, Lu L, Valencia E, Burnette JM 3rd, Okumoto Y, Wessler SR, Stajich JE. The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice. G3. 2013. 3(6):949-57. doi: 10.1534/g3.112.005348.

Abramyan J, Stajich JE. Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis. MBio. 2012 Jun 19;3(3):e00150-12. doi: 10.1128/mBio.00150-12.

Joneson S, Stajich JE, Shiu SH, Rosenblum EB.Genomic transition to pathogenicity in chytrid fungi. PLoS Pathog. 2011 Nov;7(11):e1002338. doi: 10.1371/journal.ppat.1002338

Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li W, Nayak V, Pinney DF, Stoeckert CJ Jr, Roos DS. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81. doi:10.1093/nar/gkr918.

Stajich JE, Berbee ML, Blackwell M, Hibbett DS, James TY, Spatafora JW, Taylor JW.The fungi. Current Biology. 2009;19(18):R840-5. DOI: 10.1016/j.cub.2009.07.004 

Sharpton TJ, Stajich JE, Barker B, Cole G, Gardner M, Grynberg M, Hung C, Jordar V, Maiti R, Kirkland T, Muszewska A, Neafsey DE, Kodira C, Orbach M, Mandel MA, McMahan C, Rounsley S, Wortman J, Birren BW, Henn M, Zeng Q, Galgiani J, Taylor JW. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 2009; doi: 10.1101/gr.087551.108

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