2021 Research Project List
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The establishment of high through-put sequencing workflow to detect pathogens of tomato and Capsicum seeds

Using small molecule RNA(sRNAs) as a detect target to clarify the consortia and identities of pathogens in import and export of tomato seeds. Specifically, a CLC NGS analysis system based on LINUX will be built up. Small RNAs from 5 tomato samples will be extracted and used for sequencing. The raw data of these sequences will be processed using a serial of bioinformatics tools and programs. Then an analysis workflow for deconstructing sequencing data into plant pathogen identities and a sRNA database of tomato host plant will be set up. Along with hardware updating with high-performance computing processors, this workflow will help us to establish sRNA detection procedures for tomato pathogens. Moreover, batched of import and export tomato seeds will be collected and tested. The purpose of this project is to collect and analyze small molecule RNA sequence data to establish a method for plant pathogen detection. Assisting domestic seed and seedling operators to verify the pathogens of important materials and to establish a source database of healthy species. This technology can be applied to applications for new crop varieties. Samplers can go to the exporting country to investigate the epidemic materials. Border guards can also conduct disease phase analysis for centralized input samples.

The small RNA sequencing results of seed and leaf samples of tomato and Capsicum.
Fig. 1. The small RNA sequencing results of seed and leaf samples of tomato and Capsicum.
Using RT-PCR and amplicon sequencing to confirm digital analysis results of the small RNA sequencing data.
Fig. 1. Using RT-PCR and amplicon sequencing to confirm digital analysis results of the small RNA sequencing data.