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. 2015 Nov 4;10(11):e0142221.
doi: 10.1371/journal.pone.0142221. eCollection 2015.

Large-Scale Transcriptome Analysis of Cucumber and Botrytis cinerea during Infection

Weiwen Kong  1 , Nan Chen  1 , Tingting Liu  1 , Jing Zhu  1 , Jingqi Wang  1 , Xiaoqing He  1 , Yi Jin  1
Affiliations

Large-Scale Transcriptome Analysis of Cucumber and Botrytis cinerea during Infection

Weiwen Kong et al. PLoS One. .

Abstract

Cucumber gray mold caused by Botrytis cinerea is considered one of the most serious cucumber diseases. With the advent of Hi-seq technology, it is possible to study the plant-pathogen interaction at the transcriptome level. To the best of our knowledge, this is the first application of RNA-seq to identify cucumber and B. cinerea differentially expressed genes (DEGs) before and after the plant-pathogen interaction. In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. This is the first systematic transcriptome analysis of components related to the B. cinerea-cucumber interaction. Functional genes and putative pathways identified herein will increase our understanding of the mechanism of the pathogen-host interaction.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Volcano map of differentially expressed cucumber genes.
Significantly differentially expressed genes are shown as a red (up) or green (down) dot. No significant difference between the expressions of genes is shown as a blue dot. Abscissa represents multiple genes expressed in different samples. Ordinate represents the magnitude of gene expression changes.
Fig 2
Fig 2. Volcano map of differentially expressed B. cinerea genes.
Significantly differentially expressed genes are shown as a red (up) or green (down) dot. No significant difference between the expressions of genes is shown as a blue dot. Abscissa represents multiple genes expressed in different samples. Ordinate represents the magnitude of gene expression changes.
Fig 3
Fig 3. The 30 most enriched GO terms (cucumber).
Bar chart of cucumber DEGs enriched in GO term, it can directly reflect the number of DEGs distributing into different GO terms.
Fig 4
Fig 4. The 30 most enriched GO terms (B. cinerea).
Bar chart of B.cinerea DEGs enriched in GO term, it can directly reflect the number of DEGs distributing into different GO terms.
Fig 5
Fig 5. The 20 most enriched KEGG pathways (cucumber).
“Rich factor” means that the ratio of the DEGs number and the number of genes have been annotated in this pathway. The greater of the Rich factor, the greater the degree of enrichment.
Fig 6
Fig 6. The 20 most enriched KEGG pathways (B. cinerea).
“Rich factor” means that the ratio of the DEGs number and the number of genes have been annoted in this pathway. The greater of the Rich factor, the greater the degree of enrichment.
Fig 7
Fig 7. Quantitative RT-PCR validations of five genes in cucumber and five genes in B. cinerea.
See this image and copyright information in PMC

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