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Li-Jun Ma

Assistant Professor

Office

LSL N433
(413) 545-1205

Focus

Fungal comparative genomics, eukaryotic genome evolution and organism adaptation

Background and Training

PhD: State University of New York, the College of
Environmental Sciences and Forestry
Postdoc: Harvard University

Research Summary

A dynamic genome with high plasticity contributes directly to the success of the organism to adapt to changing environments.  My lab studies genetic mechanisms that sustain structural and functional flexibility while maintaining the integrity of the organism using the model fungal system Fusarium oxysporum.

F. oxysporum is a highly adaptive species complex that consists of both plant and human pathogens. Collectively, members within this species complex cause destructive and intractable wilt diseases across a diverse spectrum of plant hosts, including numerous economically important crops: e.g., cotton, canola, melons, and tomato. During the past two decades, F. oxysporum strains have also emerged as opportunistic pathogens causing life-threatening infections in immunocompromised patients. However, any single pathogenic form exhibits strong host specificity. Comparative genomics demonstrated that horizontal transfer of pathogenicity chromosomes conveys host-specific pathogenicity (Ma et al., 2010). The pathogenicity chromosomes encoded in each pathogenic form provide a focal point for investigating the genetic mechanisms that underlie pathogenesis. F. oxysporum has also been used to study host-pathogen interactions to investigate horizontal chromosome transfer in eukaryotes.

Specifically, my research combines experimental and computational biology approaches to:

  1. Study the molecular interactions within the genome and between the “core genome” and the horizontally transferred chromosomes by reconstructing regulatory network;
  2. Investigate the plant-fungal interactions using a Fusarium-Arabidopsis pathosystem for the development of optimized management strategies to control the Fusarium vascular wilt diseases; and dissect virulence factors that contribute to emerging infectious disease using Fusarium-animal model systems for the development of novel therapeutics.
  3. Dissect virulence factors that contribute to emerging infectious disease using Fusarium-animal model systems for the development of novel therapeutics.

Publications

Ma, L.-J., D. Geiser, R. H. Proctor, A. P. Rooney, K. O’Donnell, F. Trail, D. M. Gardiner, J. M. Manners, K. Kazan. 2013. Fusarium Pathogenomics. Annual Review of Microbiology. 167: 399-416.

Manning V…..[23 co-authors],…… L.-J. Ma*, L. Ciuffetti*. 2013. Pyrenophora tritici-repentis genome reveals mechanisms that contribute to high genetic variations. G3: Genes, Genomes, Genetics. 3: 41-63.

O’Connell R.J, M.R. Thon, …, L.-J. Ma , L.J. Vaillancourt. 2012. Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics. Published online 12 August 2012. [Nature Genetics]

Amyotte S. G., X. Tan, K. Pennerman, M. del M. Jimenez, S. J. Klosterman, L.-J. Ma , K. F. Dobinson, P. Veronese. 2012. Transposable elements in the phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification. BMC Genomics. 13: 314. [BMC Genomics]

Klosterman S., K. ….. K. F. Dobinson, L.-J. Ma. 2011. Verticillium comparative genomics yields insights into niche adaptation by plant vascular wilt pathogens. PLoS Pathogen 7(7): e1002137 doi:10.1371/journal.ppat.1002137. [PubMed]

Grabherr M.G., Mauceli E., and L.-J. Ma. 2011. Genome Sequencing and Assembly. Methods Mol. Biol., 722 J.-R. Xu and B.H. Bluhm, eds. Methods in Microbiology Vol. 722. 2011. Humana Press, pp1-9.

Ma L.-J. , H. Charlotte van der Does, et al. 2010. Fusarium comparative genomics reveals lineage-specific chromosomes related to pathogenicity. Nature 465:367-373. [PubMed]
a. Post-publication peer review Faculty of 1000 [F1000]
b. Highlight in Nature Reviews Microbiology [Nature Reviews]

Kumar L., A. Breakspear, J. Menke, C. Kistler, L.-J. Ma, X. Xie. 2010. Systematic Discovery of regulatory motifs in Fusarium by comparison of four Fusarium genomes. BMC Genomics 11:208. [PubMed]

Ma L.-J. , and Fedorova, ND. A practical guide to fungal genome projects: strategy, technology, cost and completion. Mycology: An International Journal on Fungal Biology. 2010 Apr 01; 1(1): 9-24. 2010.

Ma L.-J.*, A. S. Ibrahim, C. Skory, M. G. Grabherr, G. Burger, F. Lang, A. Abe, M. Butler, et al. 2009. Genomic analysis of a basal fungus Rhizopus oryzae reveals whole genome duplication. PLoS Genet5(7): e1000549. [PubMed]