Identification of Known and Novel MicroRNAs in Raspberry Organs Through High-Throughput Sequencing.

Gengxuan Yan,Hongyi Yang,Meng Jiang,Xince Gao,Lili Li,Jie Zhang

doi:10.3389/fpls.2020.00728

Abstract

MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in plants by negatively affecting gene expression. Studies on the identification of miRNAs and their functions in various plant species and organs have significantly contributed to plant development research. In the current study, we utilized high-throughput sequencing to detect the miRNAs in the root, stem, and leaf tissues of raspberry (Rubus idaeus). A total of more than 35 million small RNA reads ranging in size from 18 to 35 nucleotides were obtained, with 147 known miRNAs and 542 novel miRNAs identified among the three organs. Sequence verification and the relative expression profiles of the six known miRNAs were investigated by stem-loop quantitative real-time PCR. Furthermore, the potential target genes of the known and novel miRNAs were predicted and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Enrichment analysis of the GO-associated biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Moreover, the miRNA target prediction revealed that most of the targets predicted as transcription factor-coding genes are involved in cellular and metabolic processes. This report is the first to identify miRNAs in raspberry. The detected miRNAs were analyzed by cluster analysis according to their expression, which revealed that these conservative miRNAs are necessary for plant functioning. The results add novel miRNAs to the raspberry transcriptome, providing a useful resource for the further elucidation of the functional roles of miRNAs in raspberry growth and development.

Highlights

Raspberry fruit has a high nutritive value, excellent flavor, and multiple health components, including ellagic acid, bioflavonoids, superoxide dismutase, and salicylic acid (Bobinaite et al, 2012)
We identified miRNAs that were highly expressed in different raspberry organs and excavated the miRNA targets and compared their relative expression among all of the samples by quantitative realtime-PCR analysis
Based on the average transcripts per million (TPM), as calculated from the three replicates of each organ, we considered mRNA with a fold change ≥ 2 and a false discovery rate (FDR) < 0.05 in a comparison as significantly differentially expressed genes (DEGs), while a fold change ≥ 2 and P < 0.05 was used for the miRNA

Summary

Introduction

Raspberry fruit has a high nutritive value, excellent flavor, and multiple health components, including ellagic acid, bioflavonoids, superoxide dismutase, and salicylic acid (Bobinaite et al, 2012). There are two fruiting types in raspberries: floricane and primocane-fruiting (Dale, 2008). The flowers bloom during late summer and early autumn, and fruiting can occur in the first year of development (Carew et al, 2015). Raspberries are mostly biennial canes (stems) on a longlived perennial rootstock, which initially forms from seedling establishment or the production of root suckers. Sterile first-year stems (primocanes) develop from buds at or below the ground surface and generally produce only leaves (Whitney, 1982). Lateral branches, known as floricanes, develop from the axils of the primocanes, and produce both leaves and fruits

Objectives

Methods

Results

Conclusion