Identification of miRNAs and Their Targets in Cotton Inoculated with Verticillium dahliae by High-Throughput Sequencing and Degradome Analysis.

Yujuan Zhang,Jie Chen,Wei Wang,Minxuan Xia,Fafu Shen,Jubo Liu

doi:10.3390/ijms160714749

Yujuan Zhang, Jie Chen + Show 4 more

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https://doi.org/10.3390/ijms160714749

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Abstract

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs that play important roles in plant growth, development, and stress response processes. Verticillium wilt is a vascular disease in plants mainly caused by Verticillium dahliae Kleb., the soil-borne fungal pathogen. However, the role of miRNAs in the regulation of Verticillium defense responses is mostly unknown. This study aimed to identify new miRNAs and their potential targets that are involved in the regulation of Verticillium defense responses. Four small RNA libraries and two degradome libraries from mock-infected and infected roots of cotton (both Gossypium hirsutum L. and Gossypium barbadense L.) were constructed for deep sequencing. A total of 140 known miRNAs and 58 novel miRNAs were identified. Among the identified miRNAs, many were differentially expressed between libraries. Degradome analysis showed that a total of 83 and 24 genes were the targets of 31 known and 14 novel miRNA families, respectively. Gene Ontology analysis indicated that many of the identified miRNA targets may function in controlling root development and the regulation of Verticillium defense responses in cotton. Our findings provide an overview of potential miRNAs involved in the regulation of Verticillium defense responses in cotton and the interactions between miRNAs and their corresponding targets. The profiling of these miRNAs lays the foundation for further understanding of the function of small RNAs in regulating plant response to fungal infection and Verticillium wilt in particular.

Highlights

MicroRNAs are a class of endogenous non-coding small RNAs that regulate gene expression at the transcriptional and post-transcriptional levels via mRNA cleavage or translational repression in plants and animals [1,2,3]
All three miRNAs negatively regulate auxin signaling by either targeting auxin receptor genes or auxin response factors [12]. Another recent study reported that miR162 and miR168 targeted Dicer-like1 and Argonaute proteins, which are likely up-regulated by infection and presumably positively regulated by plant defense responses, their functions need to be confirmed by experimental data [13]
A total of 140 known miRNAs and 58 novel miRNAs were identified and 107 genes sliced by 45 miRNA families were detected via degradome sequencing

Summary

Introduction

MicroRNAs (miRNAs) are a class of endogenous non-coding small RNAs (sRNAs) that regulate gene expression at the transcriptional and post-transcriptional levels via mRNA cleavage or translational repression in plants and animals [1,2,3]. SRNA-mediated gene silencing was found to play a significant role in plant defense against pathogens [8,11,12,13]. In Arabidopsis thaliana, miR393 was found to contribute to basal defense against Pseudomonas syringae by regulating auxin signaling [8]. All three miRNAs negatively regulate auxin signaling by either targeting auxin receptor genes or auxin response factors [12]. Another recent study reported that miR162 and miR168 targeted Dicer-like and Argonaute proteins, which are likely up-regulated by infection and presumably positively regulated by plant defense responses, their functions need to be confirmed by experimental data [13]

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