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| Status |
Public on Sep 29, 2018 |
| Title |
Transcriptomes of two phytophthora species at mycelium stage |
| Organisms |
Phytophthora infestans; Phytophthora sojae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| 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.
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| Contributor(s) |
Dong S, Chen H, Shu H |
| Citation(s) |
30382931 |
| |
| Submission date |
Jun 20, 2018 |
| Last update date |
Nov 18, 2018 |
| Contact name |
Haidong Shu |
| E-mail(s) |
2018202004@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Department |
Department of Plant Pathology
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| Lab |
The Lab of Pathogenomics
|
| Street address |
Weigang NO.1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (2) |
| GPL25217 |
Illumina HiSeq 4000 (Phytophthora sojae) |
| GPL25218 |
Illumina HiSeq 4000 (Phytophthora infestans) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA476999 |
| SRA |
SRP151012 |
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