Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (Benincasa hispida) Based on High-Throughput Sequencing

Jinqiang Yan,Min Wang,Dasen Xie,Xiaoming He,Biao Jiang,Wenrui Liu,Qingwu Peng

doi:10.3390/app112110068

Abstract

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20–24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.

Highlights

IntroductionMicroRNAs (miRNAs) are small endogenous single-stranded non-coding small RNAs of 20–24 nucleotides (nts) that negatively regulate gene expression at the post-transcriptional level [1]
The pri-RNAs are processed to generate 100–200 nt pre-miRNAs with stem-loop structures catalyzed by Dicerlike I enzyme (DCL1) in the nucleus, which creates a miRNA/miRNA* complex [5,6]. These complexes are translocated into the cytoplasm and integrated with RNA-induced silencing complex (RISC), where the miRNA strand is incorporated with RISC and the miRNA* strand is usually degraded [7]
To obtain a comprehensive knowledge of the small RNAs in wax gourd, five independent small RNA libraries from leaf, root, stem, flower, and fruit of wax gourd B227 were subjected for high-throughput sequencing

Summary

Introduction

MicroRNAs (miRNAs) are small endogenous single-stranded non-coding small RNAs of 20–24 nucleotides (nts) that negatively regulate gene expression at the post-transcriptional level [1]. The pri-RNAs are processed to generate 100–200 nt pre-miRNAs (precursor miRNAs) with stem-loop structures (hairpins) catalyzed by Dicerlike I enzyme (DCL1) in the nucleus, which creates a miRNA/miRNA* complex [5,6]. These complexes are translocated into the cytoplasm and integrated with RNA-induced silencing complex (RISC), where the miRNA strand is incorporated with RISC and the miRNA* strand is usually degraded [7]

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Results

Discussion

Conclusion