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Transcriptome analysis reveals differentially expressed genes associated with propamocarb response in cucumber (Cucumis sativus L.) fruit

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Abstract

High-throughput tag-sequencing (Tag-seq) from Illumina analysis, which is based on the Solexa Genome Analyzer platform, was applied to analyze the gene expression profiling of propamocarb (PM) treatment and control in cucumber fruit. Approximately 3.6 million complete clean sequence tags at PM treatment or control library were obtained with approximately 0.1 million distinct clean tag sequences. Approximately 41.79–43.15 % of the distinct clean tags were mapped unambiguously to the unigene database, and 32.54–33.46 % of the distinct clean tags were mapped to the cucumber genome database. The profiling analysis of the differentially expressed genes revealed the up-regulation of 546 genes and the down-regulation of 185 genes with PM response. Furthermore, the differentially expressed genes mainly linked to pesticide detoxication, response to stress/stimulus, transporter/signaling, and some important transcription factors. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) and reverse transcription polymerase chain reaction (RT-PCR) using 16 genes independently verified the tag-mapped results. The present study reveals the comprehensive mechanisms of PM response in cucumber fruit.

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Abbreviations

DAC:

Day after colonization

DEG:

Differentially expressed genes

DGE:

Digital gene expression

FDR:

False discovery rate

GO:

Gene ontology

GST:

Glutathione S-transferase

KEGG:

Kyoto Encyclopedia of Genes and Genomes

PM:

Propamocarb

POD:

Peroxidase

qRT-PCR:

Real-time quantitative RT-PCR

ROS:

Reactive oxygen species

RT-PCR:

Reverse transcription polymerase chain reaction

TPM:

Transcripts per million

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Acknowledgments

The authors greatly appreciate Prof Y. Weng and two anonymous reviewers for providing constructive suggestions on earlier version of this article. This study was financially supported by the National Natural Science Foundation of China (31272158) and 863 Program of National Science and Technology of China (2012AA100105).

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Authors and Affiliations

  1. College of Horticulture, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Northeast Agricultural University, Ministry of Agriculture, 59 Mucai Road, Harbin, 150030, People’s Republic of China

    Peng Wu, Zhiwei Qin, Wen Zhao, Xiuyan Zhou, Tao Wu, Ming Xin & Qianqian Guo

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  1. Peng Wu
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  2. Zhiwei Qin
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  3. Wen Zhao
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  4. Xiuyan Zhou
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  5. Tao Wu
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  7. Qianqian Guo
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Correspondence to Zhiwei Qin.

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Communicated by Y. Wang.

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Wu, P., Qin, Z., Zhao, W. et al. Transcriptome analysis reveals differentially expressed genes associated with propamocarb response in cucumber (Cucumis sativus L.) fruit. Acta Physiol Plant 35, 2393–2406 (2013). https://doi.org/10.1007/s11738-013-1274-1

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