Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion

Abstract

Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genus Actinidia under different situations using ribosomal RNA (rRNA) depleted RNA-Seq data. A total of 3,582 circRNAs were identified in Actinidia, of which 64.01, 21.44, and 14.55% were intergenic circRNAs, exonic circRNAs, and intronic circRNAs, respectively. Tissue-specific expression of circRNAs was observed in kiwifruit, and a species-specific response was detected when infected with Pseudomonas syringae pv. actinidiae (Psa), which is the causative agent of kiwifruit bacterial canker disease. Furthermore, we found that both exonic and intronic circRNAs were significantly positively correlated to parent protein-coding genes, and intronic circRNAs are a class of highly remarkable regulators the parent genes comparing to that of exonic circRNAs. Expression and weighted gene co-expression network analysis (WGCNA) identified a set of circRNAs that were closely associated with plant defense response. The findings of the presents study suggest that circRNAs exhibit tissue- and species-specific expression, as well as play an important role in plant immune response.

Identification and characterization of circular RNAs during the sea buckthorn fruit development

“…Past researches revealed that most circRNAs may regulated the expression level of their corresponding host genes in many species [22,29,33]. For example, circMbl can act as a competitor for linear mRNA to regulate gene function [25].…”

circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

“…circRNAs regulate gene expression in animals through different mechanisms, such as miRNA sponges, specific RNA-RNA interactions, and affecting alternative splicing . Since the identification of their roles in regulating gene expression in animals (Memczak et al, 2013), circRNAs have also been identified in different plant species, including Arabidopsis (Arabidopsis thaliana), rice, wheat (Triticum aestivum), barley (Hordeum vulgare), maize (Zea mays), tomato (Solanum lycopersicum), potato (Solanum tuberosum), soybean (Glycine max), cotton (Gossypium hirsutum), and kiwifruit (Actinidia deliciosa; Wang et al, 2014Wang et al, , 2017bWang et al, , 2017cLu et al, 2015;Ye et al, 2015Ye et al, , 2017Darbani et al, 2016;Zuo et al, 2016;Chen et al, 2017Chen et al, , 2018Zhao et al, 2017).…”

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

“…Recently, with the development of high-throughput sequencing technology, increasing numbers of circRNAs have been detected in plants and animals. In plants, circRNAs are closely related to plant development and stress responses, including biotic and abiotic stresses [20,[22][23][24][25][26][27][28]30,53]. However, whether circRNAs participate in the pathways of plant responses to hormones is unclear.…”

“…Plant circRNAs are as conserved and tissue specific as animal circRNAs, but their flanking introns do not contain as many repetitive elements and reverse complementary sequences as those in animals [15,16,19,29]. Recent studies have suggested that plant circRNAs play functional roles in developmental processes and stress responses, including the responses to drought, chilling injury, nutrient deficiency, and pathogen invasion [19,20,22,24,25,30]. Based on the functions of animal circRNAs, circRNA-miRNA-mRNA networks have been generated for plants; these networks suggest that plant circRNAs may act as miRNA sponges to regulate functional gene expression [23,25,31].…”