GSE116090
Transcriptomes of two phytophthora species at mycelium stage
Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. sojae P6497. Read counts was calculated using featureCounts, and DEGs was calculated using DEseq2 with |log2FC|=1, y-axis is FDR<0.05. Conclusions: 6mA is associated with lowly expressed genes. Examination of differentially expressed genes (DEGs) in psdamt3 uncovers a total of 3156 genes, with 1544 genes up-regulated and 1622 genes down-regulated. Overall design: mRNA profiles of Phytophthora sojae P6497 mycelium (WT,3-days old),PsDAMT3 mycelium(mu,3-days old)and Phytophthora infestans T30-4 mycelium (6-days old) were generated by deep sequencing, in two or three replicates.