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.
No subject area
Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification (with Stefan G. Amyotte, Xiaoping Tan, Kayla Pennerman, Maria del Mar Jimenez-Gasco, Steven J. Klosterman, Katherine F. Dobinson, and Paola Veronese), BMC Genomics (2012)
Background Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive...
Empower research through comparative genomics & next-gen sequencing, Clinical and Translational Science Research Retreat (2012)
Describes research in comparative fungal genomics, specifically the the plant-fungal interactions of wilt diseases caused...
Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens (with Steven J. Klosterman, Krishna V. Subbarao, Seogchan Kang, Paola Veronese, Scott E. Gold, Bart P. H. J. Thomma, Zehua Chen, Bernard Henrissat, Yong-Hwan Lee, Jongsun Park, Dez J. Barbara, Maria D. Garcia-Pedrajas, Amy Anchieta, Ronnie de Jonge, Parthasarathy Santhanam, Karunakaran Maruthachalam, Zahi Atallah, Stefan G. Amyotte, Zahi Paz, Patrik Inderbitzin, Ryan J. Hayes, David I. Heiman, Sarah Young, Qiandong Zeng, Reinhard Engels, James Galagan, Christina A. Cuomo, and Katherine F. Dobinson), PLoS Pathogens (2011)
The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing...
Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes (with Lokesh Kumar, Andrew Breakspear, Corby Kistler, and Xiaohui Xie), BMC Genomics (2010)
Background
Fusarium graminearum (Fg), a major fungal pathogen of cultivated cereals, is responsible for billions...
Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication (with Ashraf S. Ibrahim, Christopher Skory, Manfred G. Grabherr, Gertraud Burger, Margi Butler, Marek Elias, Alexander Idnurm, B. Franz Lang, Teruo Sone, Ayumi Abe, Sarah E. Calvo, Luis M. Corrochano, Reinhard Engels, Jianmin Fu, Wilhelm Hansberg, Jung-Mi Kim, Chinnappa D. Kodira, Michael J. Koehrsen, Bo Liu, Diego Miranda-Saavedra, Sinead O'Leary, Lucila Ortiz-Castellanos, Russell Poulter, Julio Rodriguez-Romero, José Ruiz-Herrera, Yao-Qing Shen, Qiandong Zeng, James Galagan, Bruce W. Birren, Christina A. Cuomo, and Brian L. Wickes), PLoS Genetics (2009)
Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid...