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Genome-wide identification of cucumber green mottle mosaic virus-responsive microRNAs in watermelon

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Abstract

Cucumber green mottle mosaic virus (CGMMV) is a damaging pathogen that attacks crop plants belonging to the family Cucurbitaceae. Little is known about the regulatory role of microRNAs (miRNAs) in response to CGMMV infection. To identify CGMMV-responsive miRNAs, two sRNA libraries from mock-inoculated and CGMMV-infected watermelon leaves were constructed and sequenced using Solexa sequencing technology. In total, 471 previously known and 1,809 novel miRNAs were obtained, of which 377 known and 246 novel miRNAs were found to be differentially expressed during CGMMV infection. The target genes for the CGMMV-responsive known miRNAs are active in diverse biological processes, including cell wall modulation, plant hormone signaling, defense-related protein induction, primary and secondary metabolism, regulation of virus replication, and intracellular transport. The expression patterns of some CGMMV-responsive miRNAs and their corresponding targets were confirmed by RT-qPCR. One target gene for miR156a-5p was verified by 5’-RNA-ligase-mediated rapid amplification of cDNA ends (5’-RLM-RACE) analysis. The results of this study provide further insights into the miRNA-mediated regulatory network involved in the response to viral infection in watermelon and other cucurbit crops.

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Acknowledgements

This work was funded by grants from the China Postdoctoral Science Foundation (2016M601973), the National Natural Science Foundation of China (31572145).

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  1. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People’s Republic of China

    Yuyan Sun, Xiaowei Niu & Min Fan

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  1. Yuyan Sun
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Correspondence to Yuyan Sun or Min Fan.

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Electronic supplementary material

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Supplementary material 1 Fig. S1 Secondary structure prediction of novel miRNAs precursors (PDF 1401 kb)

705_2017_3401_MOESM2_ESM.doc

Supplementary material 2 Table S1 Primers used for quantification and validation of selected watermelon CGMMV responsive miRNAs and their targets (DOC 35 kb)

Supplementary material 3 Table S2 Known miRNA identified from mock and CGMMV libraries (XLSX 47 kb)

705_2017_3401_MOESM4_ESM.xlsx

Supplementary material 4 Table S3 Novel miRNA precursor candidates identified from mock and CGMMV libraries (XLSX 482 kb)

Supplementary material 5 Table S4 Unique novel miRNA sequences generated from mock and CGMMV libraries (XLSX 134 kb)

Supplementary material 6 Table S5 miRNAs that are differentially expressed after CGMMV infection (XLSX 58 kb)

Supplementary material 7 Table S6 Target prediction for differentially expressed known miRNAs (XLSX 30 kb)

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Sun, Y., Niu, X. & Fan, M. Genome-wide identification of cucumber green mottle mosaic virus-responsive microRNAs in watermelon. Arch Virol 162, 2591–2602 (2017). https://doi.org/10.1007/s00705-017-3401-6

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