Submitted by Ksenia Krasileva on
Fungal plant pathogens pose a great threat to food security worldwide by causing major yield losses in agriculture. While the development of genetically modified crops that are resistant to these diseases offers an appealing solution, these often only have short term impacts as the pathogens can rapidly adapt to these new defenses. A better understanding of how these pathogens adapt to plant defenses so quickly is vital to implementing disease prevention strategies in the future.
Genomic studies have revealed many interesting characteristics of fungal plant pathogen genomes that could contribute to their adaptability including accessory chromosomes, lineage specific genomic compartments, and the prevalence of transposable elements (TEs). We are interested in gaining a more mechanistic understanding of this adaptability with the hypothesis that TEs actively and passively contribute to genomic plasticity in these fungi.
This project will start with identifying the location and identity of TEs in the genome of Magnaporthe oryzae, the causal agent of the rice blast disease and one of the most important pathogens in agriculture today. We will then answer the following questions:
How does TE content vary between strains of M. oryzae?
How do TEs contribute to the evolution of disease-causing genes in M. oryzae?
How does TE activity change during different stages of infection?
Skills the student will learn through this project include, but are not limited to:
Using bioinformatics software on the command line
Writing scripts in bash to automate data processing and visualization
High performance computing and usage of the UC Berkeley computing cluster
Understanding of genomics and computational biology
The roles of different researchers in the lab, including undergraduate students are described in Krasileva Lab Charter (link)
The student must be a 2nd year or above with a good understanding of genetics and molecular biology. No prior experience required but familiarity with computers and troubleshooting is greatly appreciated as well as any experience with coding. Student should be highly motivated and willing to work independently but not afraid to ask many questions. Student should also be prepared and willing to contribute own ideas and experiments to the project once the project is well under way. The student is expected to dedicate approximately 10 hours a week to the project with flexible hours aside from weekly Zoom meetings with the mentor.