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Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing

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Abstract

MicroRNAs (miRNAs) play important regulatory roles in plant development and stress responses. Tomato is an economically important vegetable crop in the world with publicly available genomic information database, but only a limited number of tomato miRNAs have been identified. In this study, two independent small RNA libraries from mock and Cucumber mosaic virus (CMV)-infected tomatoes were constructed, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 plant miRNAs and 273 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 plant miRNAs and 82 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed that 79 miRNAs (including 15 new tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries, and the expression patterns of some new tomato miRNAs and PC-miRNAs were further validated by qRT-PCR. Moreover, potential targets for some of the known and new tomato miRNAs were identified by the recently developed degradome sequencing approach, and target annotation indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that defense response- and photosynthesis-related genes were most affected in CMV-Fny-infected tomatoes. Because tomato is not only an important crop but also is a genetic model for basic biology research, our study contributes to the understanding of miRNAs in response to virus infection.

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Abbreviations

CMV:

Cucumber mosaic virus

AGO:

Argonaute

DCL:

Dicer-like

nt:

Nucleotide

miRNA:

MicroRNA

siRNA:

Small interfering RNA

pri-miRNA:

Primary miRNA

pre-miRNA:

miRNA precursor

RISC:

RNA-induced silencing complex

dpi:

Days post-inoculation

MFEI:

Minimal folding free energy index

PC-miRNA:

Potential candidate miRNA

qRT-PCR:

Reverse transcription-quantitative polymerase chain reaction

C t :

Threshold cycle

T-plots:

Target plots

GO:

Gene ontology

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Acknowledgments

This work was supported by the grants from the National Natural Science Foundation of China (30800716) and the Science Foundation of Zhejiang Sci-Tech University (ZSTU) under Grant No. 1016816-Y.

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Authors and Affiliations

  1. Institute of Aquatic Products Processing, College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, 310035, China

    Junli Feng

  2. College of Life Science, Zhejiang Sci-Tech University, Hangzhou, China

    Shasha Liu & Mengna Wang

  3. LC Sciences, Houston, TX, USA

    Qiulei Lang & Chunzhi Jin

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  1. Junli Feng
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  2. Shasha Liu
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  3. Mengna Wang
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  4. Qiulei Lang
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Corresponding author

Correspondence to Junli Feng.

Electronic supplementary material

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Supplementary Table S1

Primers used for qRT-PCR in this study. Supplementary material 1 (XLS 48 kb)

Supplementary Table S2

Profile of the known tomato microRNAs (miRBase 20.0) identified in this study. Supplementary material 2 (XLS 96 kb)

Supplementary Table S3

Profile of microRNAs originating from other plant pre-miRNAs (miRBase 20.0) that can be mapped to tomato genome. Supplementary material 3 (XLS 70 kb)

Supplementary Table S4

Profile of microRNAs originating from pre-miRNAs that cannot be mapped to tomato genome, but the microRNAs were mapped to tomato genome and the extended sequences at the mapped positions of the genome potentially form hairpins. Supplementary material 4 (XLS 85 kb)

Supplementary Table S5

50 new tomato miRNAs belonging to 32 known plant miRNA families identified in this study. Supplementary material 5 (XLS 70 kb)

Supplementary Table S6

Profile of candidate miRNAs originating from predicted RNA hairpins (PC-type pre-miRNAs). Supplementary material 6 (XLS 141 kb)

Supplementary Table S7

82 PC-miRNAs were identified with both the 3p and 5p strands in this study. Supplementary material 7 (XLS 86 kb)

Supplementary Table S8

Profile of differently expressed microRNAs between the two libraries. Supplementary material 8 (XLS 105 kb)

Supplementary Table S9

Profile of PC-miRNAs, which were differently expressed between the two libraries. Supplementary material 9 (XLS 75 kb)

Supplementary Table S10

Targets of all tomato miRNAs identified in this study and their function verified by degradome sequencing. Supplementary material 10 (XLS 157 kb)

Supplementary Table S11

Function for the targets of new tomato miRNAs and PC-miRNAs verified by degradome sequencing. Supplementary material 11 (XLS 81 kb)

Supplementary Table S12

GO analyses of the targets for known and new tomato miRNAs. Supplementary material 12 (XLS 1,801 kb)

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Feng, J., Liu, S., Wang, M. et al. Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing. Planta 240, 1335–1352 (2014). https://doi.org/10.1007/s00425-014-2158-3

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  • DOI: https://doi.org/10.1007/s00425-014-2158-3

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