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.
| Accession | PRJNA476999; GEO: GSE116090 |
| Data Type | Transcriptome or Gene expression |
| Scope | Multispecies |
| Publications | Chen H et al., "Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions.", Genome Biol, 2018 Oct 31;19(1):181 |
| Submission | Registration date: 20-Jun-2018
The Lab of Pathogenomics, Department of Plant Pathology, Nanjing Agricultural University |
| Relevance | Environmental |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 7 |
| Publications |
| PubMed | 1 |
| PMC | 1 |
| Other datasets |
| BioSample | 7 |
| GEO DataSets | 1 |