Limits...
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.


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.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4633151&req=5

pone.0142221.g001: 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.

Mentions: The expected number of reads per kilobase of transcript sequence per million base pairs sequenced (RPKM) is the most common method with which to estimate the level of gene expression [25]. TMM was used to standardize the read count data obtained from the last step, and DEGSeq was used to examine the differential gene expression profile between the control and treated samples. There was a total of 3,512 DEGs in the plants; 1,753 DEGs were upregulated and 1,939 were downregulated (Fig 1). There was a total of 1,735 DEGs in the pathogen; 980 DEGs were upregulated and 755 were downregulated (Fig 2). Detailed DEGs for both C. sativus L. and B. cinerea are provided in S2 and S3 Tables.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142221.g001: 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.
Mentions: The expected number of reads per kilobase of transcript sequence per million base pairs sequenced (RPKM) is the most common method with which to estimate the level of gene expression [25]. TMM was used to standardize the read count data obtained from the last step, and DEGSeq was used to examine the differential gene expression profile between the control and treated samples. There was a total of 3,512 DEGs in the plants; 1,753 DEGs were upregulated and 1,939 were downregulated (Fig 1). There was a total of 1,735 DEGs in the pathogen; 980 DEGs were upregulated and 755 were downregulated (Fig 2). Detailed DEGs for both C. sativus L. and B. cinerea are provided in S2 and S3 Tables.

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.