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| Status |
Public on Feb 13, 2018 |
| Title |
Transcriptome profiling and digital gene expression analysis of sweet potato challenged with Fusarium oxysporum f. sp.batatas. |
| Organism |
Ipomoea batatas |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of sweet potato challenged with Fob using Illumina Hiseq technology. A total of 89,944,188 clean reads were generated and were assembled into 101,988 unigenes with an average length of 666bp, 62,605(61.38%) of them were functional annotated in the non-redundant(nr) protein database from NCBI by using BLASTX with a cut-off E-value of 10-5, and COG,GO and KEGG annotations were examined for better understand their functions. Five DGE libraries were constructed from the sweet potato cultivar JS57 (high resistance) and XZH (high susceptible) challenged with pathogenic and Nonpathogenic Fob. The differentially expressed genes including up- and down-regulation in five libraries were identified and calculated based on comparisons of transcriptomes, showing differences in gene expression profiles among the samples. A set of differentially expressed genes involved disease response were identified, including 40 WRKY and seven NAC transcription factors, four resistance genes, 22 pathogenesis-related genes, and six genes involved in SA signal pathway. Our study is the first to provide the transcriptome sequence resource of sweet potato challenged with pathogenic and non-pathogenic Fob and demonstrate its digital expression profiling. We discovered a set of genes involved in disease resistance. These data provides comprehensive sequence resource of sweet potato for genetic and genomic studies and will accelerate the understanding of molecular mechanism of disease resistance.
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| Overall design |
There were five sample groups were prepared in this experiment:
(1) JS57 inoculated with Fob-07 (JS57-F07); (2) JS57 inoculated with Fob-04 (JS57-F04); (3) JS57 in water (JS57-CK); (4) XZH inoculated with Fob-07 (XZH-F07); (5) XZH in water(XZH-CK).
Total RNAs were isolated and mixed equally to create a RNA pool for cDNA library, then the transcriptome was generated using Illumina HiSeq 2500 sequencing.
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| Contributor(s) |
Chen X, Lin Y, Zou W, Zhang Z, Onofua D, Lin S, Wang S, Yang Z |
| Citation(s) |
29131830 |
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| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuanyang Chen |
| E-mail(s) |
cxy@fafu.edu.cn
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| Organization name |
Fujian Agriculture and Forestry University
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| Street address |
15,Shangxiadian road,cangshan district
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| City |
Fuzhou |
| ZIP/Postal code |
350002 |
| Country |
China |
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| Platforms (1) |
| GPL22614 |
Illumina HiSeq 2500 (Ipomoea batatas) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA351255 |
| SRA |
SRP092253 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89290_RAW.tar |
8.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE89290_Trinity.fasta.gz |
36.6 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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