This Project focuses on determining the DNA methylation and DNA repair machinery in the stem rust Pgt 21-0. First, we identified the proteins that are responsible for carrying DNA methylation and DNA epair in Pgt genome and their expression. Next, we compared the CpG collected by Nanopolish and 5mC and 6mA methylation data collected by tombo by performing a correlation matrix to identify the similarity among the data sets.
Secondly, we determined the dominant methylation pattern that Pgt genome has by looking at the dinucleotide context in both developmental stages (germinated spores and infection day 7). Thirdly, we determined whether genes were highly expressed if 5mC resided in gene body and 6mA resided in transcription start site (TSS) by looking at genomic features (genes, promotors, transcription start site).
Lastly, we determined if TEs affect the neighboring genes expression by looking at TEs that were residing in 1kb windoow closer to genes than the genes that were not.