Postdoctoral Research fellowship Miller Institute for Basic Research in Science, 2006-2009

NSF Graduate fellowship 2003-2006

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-glucan.  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 are working to study how these genes evolved across the fungal kingdom to learn when and how some innovations of cellular forms evolved and how this relates to evolutionary history of other organisms.

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 (e.g. Synchytrium endobioticum) and we will use genome sequencing and comparative genomics to catalog differences and similarities among pathogenic lineages.

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.

A collection of cellular processes control gene expression.  The role of smallRNAs in the control of gene expression in fungi remains an area of exploration.  We are working with Neurospora crassa and Coprinopsis cinerea to learn how smallRNAs may regulate gene expression during development and control expression of other genomic elements.

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 maintence that will help delineate what is required to form multicellular structures in the extant fungi.

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, Histoplasma capsulatum, Cryptococcus, Aspergillus fumigatus, Candida, Rhizopus oryzae, Penicllium marneffei) 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.

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

Selected Research Articles

1. 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 Publisher's site
2. 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 
3. Rosenblum EB, Stajich JE, Maddox N, Eisen MB. Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. Proc Nat Acad Sci. 2008; 105(44):17034-
   17039. DOI:10.1073/pnas.0804173105
   
4. Martin F, Aerts A, Ahren D, Brun A, Duchaussoy F, Kohler A, Lindquist E, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Buee M, Brokstein P, Canback B, Cohen D, Courty PE, Coutinho PM, Danchin EGJ, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Gibon J, Grimwood J, Hoegger P, Jain P, Kilaru S, Labbe J, Lin YC, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita H, Oudot-Le Secq MP, Pereda V, Peter M, Quesneville H, Rajashekar B, Reich M, Rombauts S, Rouhier N, Schmutz J, Chalot M, Sanders I, Henrissat B, van de Peer Y, Tuskan G, Pukkila P, Stajich JE, Kues U, Polle A, Tunlid A, Podila G, Rouze P, Richardson PM, and Grigoriev IV. Symbiosis insights from the genome of the mycorrhizal basidiomycete Laccaria bicolor. Nature. 2008; 452(7183):88-92. DOI:10.1038/nature06556
5. Stajich JE, Dietrich FS, and Roy SW. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biology. 2007; 8(10):R223. DOI:10.1186/gb-2007-8-10-r223
6. Fitzpatrick DA, Logue ME, Stajich JE, and Butler G. A Fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology. 2006; 6:99. DOI:10.1186/1471-2148-6-99
7. Kamper J, Kahmann R, Bolker M, Ma L-J, Saville BJ, Banuett F, Kronstad JW, Gold SE, Brefort T, Muller O, Perlin MH, Wosten HAB, de Vries R, Ruiz-Herrera J, Reynaga-Pena CG, Snetselaar K, McCann M, Perez-Martın J, Feldbrugge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, Gonzalez-Prietro JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Scherer M, Vranes M, Ladendorf O, Fuchs U, Sandrock B, Meng S, Ho ECH, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Hauser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schluter T, Platt D, Swimmer C, Gnirke A, Chen A, Vysotskaia V, Mannhaupt G, G¨ uldener U, Munsterkotter M, Haase D, Mewes H, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DD, Calvo S, Nusbaum C, Galagan J, and Birren BW. Insights from the genome of the biotrophic fungus Ustilago maydis. Nature. 2006; 444(7115):97-101. DOI:10.1038/nature05248
8. James TY, Kauff F, Schoch C, Matheny PB, Hofstetter V, Cox CJ, Celi C, Celio G, Guiedan C, Fraker E, Miadlikowska JM, Lumbsh T, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O’Rourke B, Binder M, Curtis JM, Slot JC, Wang Z, Wilson AW, Schußler A, Longcore JE, O’Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Bude B, Geiser DM, Aptroot A, Buck WR, Cole MS, Diederich P, Hillis DM, Printzen C, Schmitt I, Schultz M, Yahr R, Zavarzin A, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, and Vilgalys R. Reconstructing the early evolution of the Fungi using a six gene phylogeny. Nature. 2006; 443(7113):818-822. DOI:10.1038/nature05110
9. Stajich JE and Dietrich FS. Evidence of mRNA Mediated Intron loss in the human pathogenic fungus Cryptococcus neoformans. Eukaryotic Cell. 2006; 5(5):789-793. DOI:10.1128/EC.5.5.789-793.2006
10. Fraser JA, Giles SS, Wenink EC, Geunes-Boyer SG, Diezmann S, Allen A, Stajich JE, Dietrich FS, Perfect JR, and Heitman J. Same-sex mating and the origin of the Vancouver island Cryptococcus gattii outbreak. Nature. 2005; 437(7063):1360-1364. DOI:10.1038/nature04220
    
11. Hahn MW, De Bie T, Stajich JE, Nguyen C, and Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research. 2005; 15(8):1153-1160. DOI:10.1101/gr.3567505
    
12. Stajich JE and Hahn MW. Disentangling the effects of demography and selection in human history. Mol Biol Evol 2005; 22:63-73. DOI:10.1093/molbev/msh252
13. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, and Waterston RH. The Genome Sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biology. 2003; 1(2):E45. DOI:10.1371/journal.pbio.0000045
14. Hahn, MW, Stajich JE, and Wray GA. The effects of selection against spurious transcription factor
    binding sites. Mol Biol Evol. 2003; 20(6):901-6. DOI:10.1093/molbev/msg096
15. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gibert JGR, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, and Birney E. The Bioperl Toolkit: Perl modules for the life sciences. Genome Research. 2002; 12(10):1611-8. DOI:10.1101/gr.361602
16. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, and Lewis S. The generic genome browser: a building block for a model organism system database. Genome Research. 2002; 12(10):1599-610. DOI:10.1101/gr.403602