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

Kong W, Chen N, Liu T, Zhu J, Wang J, He X, Jin Y - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Biological Sciences and Technology, P. O. Box 162, Beijing Forestry University, Beijing 100083, China.

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.

No MeSH data available.


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.
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pone.0142221.g004: 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.

Mentions: In the category of biological process of the pathogen, most DEGs were enriched in “single-organism transport”, “metabolic process”, “transmembrane transport”, “single-organism metabolic process”, and “oxidation-reduction process.” “Integral to membrane” was the dominant subcategory of the cellular component category. In the molecular function category, “catalytic activity”, “oxidoreductase activity”, and “oxidoreductase activity” have shown significant proportions (Fig 4). We also observed genes corresponding to “cell wall modification” GO terms, which had been investigated previously.


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

Kong W, Chen N, Liu T, Zhu J, Wang J, He X, Jin Y - PLoS ONE (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633151&req=5

pone.0142221.g004: 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.
Mentions: In the category of biological process of the pathogen, most DEGs were enriched in “single-organism transport”, “metabolic process”, “transmembrane transport”, “single-organism metabolic process”, and “oxidation-reduction process.” “Integral to membrane” was the dominant subcategory of the cellular component category. In the molecular function category, “catalytic activity”, “oxidoreductase activity”, and “oxidoreductase activity” have shown significant proportions (Fig 4). We also observed genes corresponding to “cell wall modification” GO terms, which had been investigated previously.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Biological Sciences and Technology, P. O. Box 162, Beijing Forestry University, Beijing 100083, China.

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.

No MeSH data available.