Background and Training
PhD: State University of New York, the College of
Environmental Sciences and Forestry
Postdoc: Harvard University
The focus of my laboratory is to understand genomic plasticity that enables organism niche adaptation using a model fungal system Fusarium oxysporum.
Genomic plasticity contributes directly to the adaptability of an organism to survive in changing environments. My research group studies eukaryotic genome evolution with a focus on understanding the genetic mechanisms that sustain structural and functional flexibility while maintaining the integrity of the organism. F. oxysporum is a highly adaptive species complex that consists of members that 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 such 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 and have established F. oxysporum as an effective model to investigate horizontal chromosome transfer in eukaryotes.
Specifically, we will combine the experimental and computational biology approaches to:
- study the molecular interactions between the “core genome” and the horizontally transferred chromosomes by probing regulatory network;
- investigate the plant-fungal interactions using a Fusarium-Arabidopsis pathosystem; and
- optimize management strategies to control the Fusarium diseases.
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]