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

Professor & 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

Studies of evolution in fungi using genomic tools

Multiple projects focus on using genome and transcriptome sequencing to study the evolutionary history and changes in Fungi through time. One set of projects focuses on the zygomycetes (Mucoromycota and Zoopagomycota) and chytrid fungi (Chytridiomycota, Blastocladiomycota).  Current projects include the zygomycete genealogy of life project and Phylogenomic study of the Anaerobic Gut Fungi (Neocallomasticomycota) both support by the National Science Foundation.

We co-lead the 1000 Fungal genomes project to generate 1000(s) of fungal genomes from the kingdom and efforts to analyze the genome evolution of the lineages, resolve the phylogenetic relationships of these species using phylogenomic approaches. We are using these data to ask questions about the origins of novelty in cellular morphology including the emergence of multicellular characteristics in fungi

Extremophile and desert fungi
A relatively new project in the lab is an effort to characterize the fungi, cyanobacteria, and eukaryotic algae that make up biological soil crusts in deserts. Related to this project are work sequencing genomes of extermophile fungi such as the halotolerant Hortaea werneckii and a collection of rock inhabiting species from Antarctica and desert environments.Human pathogenic fungi.

Human pathogenic fungi
The lab is engaged a project on genomics of Coccidioides in California through the UC Valley Fever Initiative with UCSF, UC Berkeley, UC Merced, and UC San Diego supported by the UCOP Multicampus Research Initiative.

A second project on population genomics of Candida (Clavispora) lusitaniae using whole genome sequencing and genetics to examine changes in fungal communities in chronic infections. This work is collaboration with Dr Deborah Hogan at Dartmouth University and supported by the National Institutes of Health.

A third project on the evolution of virulence and biology of hypoxia adaptation in Aspergillus fumigatus in collaboration with Dr Robert Cramer at Dartmouth University.

Transposable elements and their impact on genomes
Collaborative project focuses on transposable element bursts in a variety of rice in collaboration with Dr Susan Wessler at UCR.

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)

Sinha S, Flibotte S, Neira M, Formby S, Plemenitaš A, Cimerman NG, Lenassi M, Gostinčar C, Stajich JE, Nislow C. Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure.G3 (Bethesda). 2017;7(7):2015-2022. doi: 10.1534/g3.117.040691.

Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. Widespread adenine N6-methylation of active genes in fungi. Nat Genet. 2017;49(6):964-968. doi: 10.1038/ng.3859.

Nguyen TA, Cissé OH, Yun Wong J, Zheng P, Hewitt D, Nowrousian M, Stajich JE, Jedd G. Innovation and constraint leading to complex multicellularity in the Ascomycota. Nat Commun. 2017;8:14444. doi: 10.1038/ncomms14444.

Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, Bonito G, Corradi N, Grigoriev I, Gryganskyi A, James TY, O'Donnell K, Roberson RW, Taylor TN, Uehling J, Vilgalys R, White MM, Stajich JE. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016;108(5):1028-1046.

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.

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, 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 

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