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cse185-spring18-week1

CSE185 Spring 2018 Lab Assignment

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devirus

Many of plants diseases, which cause huge loss to agriculture, are caused by virus infection. System-level transcriptomic studies could help us to learn the differential expression gene (DEG) in the response to the viral infection. Though the point of view from DEG, we could get a better understanding of how the virus affect the host plant and how the plant hosts response to viral infection. It could help us develop better strategies to control the diseases. Nicotiana tabacum is also known as cultivated tobacco, which leaves could be processed into tobacco. It is one of the most common cash crop all across the world. Cucumber mosaic virus (CMV) is a vital plant pathogenic virus. It has a wide range of plant hosts. As a result, studying the genome expression change in N. tabacum after CMV infection is quite meaningful. In our study, we will use de novo transcriptome assembly strategy to build the whole transcriptome, and use it as a reference to do DEG analysis. CMV is a kind of (+) RNA virus, so there won’t an insertion in plant genome during the infection. As a consequence, we can adopt mapping first strategy (use the reference from database directly rather than assembled by our self) to do DEG and compare the performances of the two different strategy. After the DEG analysis, we could compare the difference in the genome of N. tabacum with and without infection. In addition, with the help of de novo transcriptome assembly strategy, we can rebuild the viral mRNA to viral transcriptome and find the virus. Our pipeline is appropriate to find DEG and virus in any virus caused plant disease cases.

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