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High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans

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Abstract

Main conclusion

The characterization and compare expression profiling of the miRNA transcriptome lay a solid foundation for unraveling the complex miRNA-mediated regulatory network in tomato resistance mechanisms against LB.

MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs with 20–24 nt. They have been identified in many plants with their diverse regulatory roles in biotic stresses. The knowledge, that miRNAs regulate late blight (LB), caused by Phytophthora infestans, is rather limited. In this study, we used miRNA-Seq to investigate the miRNA expression difference between the tomatoes treated with and without P. infestans. A total of 42,714,516 raw reads were generated from two small RNA libraries by high-throughput sequencing. Finally, 207 known miRNAs and 67 new miRNAs were obtained. The differential expression profile of miRNAs in tomato was further analyzed with twofold change (P value ≤0.01). A total of 70 miRNAs were manifested to change significantly in samples treated with P. infestans, including 50 down-regulated miRNAs and 20 up-regulated miRNAs. Moreover, a total of 73 target genes were acquired for 28 differentially expressed miRNAs by psRNATarget analysis. By enrichment pathway analysis of target genes, plant–pathogen interaction was the most highly relevant pathway which played an important role in disease defense. In addition, 30 miRNAs were selected for qRT-PCR to validate their expression patterns. The expression patterns for targets of miR6027, miR5300, miR476b, miR159a, miR164a and miRn13 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. The targets have previously been reported to be related with plant immune and involved in plant–pathogen interaction pathway in this study, suggesting these miRNAs might act as regulators in process of tomato resistance against P. infestans. These discoveries will provide us useful information to explain tomato resistance mechanisms against LB.

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Abbreviations

BGI:

Beijing Genomics Institute

CMV:

Cucumber mosaic virus

Cs:

Control samples

ETI:

Effector-triggered immunity

GO:

Gene Ontology

HR:

Hypersensitive response

KEGG:

Kyoto Encyclopedia of Genes and Genomes

LB:

Late blight

MFE:

Minimum free energy

MiRNA:

MicroRNA

qRT-PCR:

Reverse transcription-quantitative polymerase chain reaction

Rpi gene:

Resistance genes against P. infestans

rRNA:

Ribosomal RNA

snoRNA:

Small nuclear RNA

snRNA:

Small nuclear ribonucleic acids

TMV:

Tobacco mosaic virus

ToMV:

Tomato mosaic virus

tRNA:

Transfer RNA

Ts:

Treated samples

TuMV:

Turnip mosaic virus

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Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (Nos. 31272167, 31471880 and 61472061). We thank Prof. Weixing Shan from Northwest A&F, University of China for providing the pathogen materials.

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Authors and Affiliations

  1. School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China

    Yushi Luan, Jun Cui, Junmiao Zhai, Jie Li & Lu Han

  2. School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China

    Jun Meng

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  1. Yushi Luan
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Correspondence to Jun Meng.

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Luan, Y., Cui, J., Zhai, J. et al. High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans . Planta 241, 1405–1416 (2015). https://doi.org/10.1007/s00425-015-2267-7

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