scholarly journals The Sequence and Integrated Analysis of Competing Endogenous RNAs Originating from Tea Leaves Infected by the Pathogen of Tea Leaf Spot, Didymella segeticola

Plant Disease ◽  
2021 ◽  
Author(s):  
Yu Wang ◽  
Yuanyou Yang ◽  
Xinyue Jiang ◽  
yuqin Yang ◽  
Shilong Jiang ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Target Genes ◽  
Gene Annotation ◽  
Future Research ◽  
Circular Rnas ◽  
Integrated Analysis ◽  
Xyloglucan Endotransglycosylase ◽  
Tea Leaves ◽  
Competing Endogenous Rnas ◽  
Tea Leaf

Tea leaf spot, caused by Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai, is an important disease, which negatively affects the productivity and the quality of tea leaves. During infection by the pathogen, competing endogenous RNAs (ceRNAs) from tea leaves could contribute to achieving pathogenicity. In this study, circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), constituting ceRNAs, which share binding sites on microRNAs (miRNAs), and messenger RNAs (mRNAs), from infected and uninfected leaves of tea (Camellia sinensis cv. Fuding-dabaicha) were sequenced and analyzed, and the identity and expression levels of the target genes of miRNA-mRNA and miRNA-lncRNA/circRNA were predicted. Analysis indicated that ten mRNAs were bound by 18 miRNAs, 66 lncRNAs were bound by 40 miRNAs, and 29 circRNAs were bound by 17 miRNAs, respectively. For the regulation modes of ceRNAs, five ceRNA pairs were identified by the correlation analysis of lncRNA–miRNA–mRNA. For instance, expression of the xyloglucan endotransglycosylase (XET) gene in infected leaves was down-regulated at the level of mRNA through miRNA PC-5p-3511474_3 binding with lncRNA TEA024202.1:MSTRG.37074.1. Gene annotation indicated that expression of this gene was significantly enriched in cell wall biogenesis and in the pathway of plant hormone signal transduction. The functional analysis of ceRNAs isolated from infected tea leaves will provide a valuable resource for future research on D. segeticola pathogenicity.

scholarly journals Functional Annotation of circRNAs of Tea Leaves during the Infection by the Tea Leaf Spot Pathogen, Didymella segeticola

2021 ◽  
Author(s):  
Shilong Jiang ◽  
Yuanyou Yang ◽  
Di Guo ◽  
Yu Wang ◽  
Honglin Huang ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Functional Annotation ◽  
Differentially Expressed ◽  
Future Research ◽  
Circular Rnas ◽  
Tea Leaves ◽  
Illumina Hiseq ◽  
Host Pathogen ◽  
Plant Pathogen Interaction ◽  
Tea Leaf

Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola) is an important phytopathogen that causes leaf spot on tea, Camellia sinensis [L.] O. Kuntze, which results in huge tea production losses. The functional annotation and analysis of circular RNAs (circRNAs) of tea leaves during D. segeticola infection may reveal the host–pathogen interaction mechanisms. In this study, a model of tea (C. sinensis ‘Fuding-dabaicha’) leaves infected by D. segeticola was constructed, and then circRNAs of tea leaves were sequenced on the Illumina HiSeq 4000 platform. In total, 231 and 118 differentially expressed circRNAs from tea leaves were significantly up- and down-regulated, respectively, by the D. segeticola infection. A Kyoto Encyclopedia of Genes and Genomes analysis indicated that the differentially expressed circRNA-hosting-genes were significantly enriched in the plant–pathogen interaction pathway. As the differentially expressed circRNA-hosting-gene of circRNA in the pathway, the U-box domain-containing protein 35 gene was enriched in response to stress according to a Gene Ontology analysis. The expression profiling of circRNAs and the annotation of circRNA-hosting-genes of tea leaves during D. segeticola infection will provide a resource for future research on host–pathogen interactions.

scholarly journals Integrated mRNA and small RNA sequencing for analyzing tea leaf spot pathogen Lasiodiplodia theobromae, under in vitro conditions and the course of infection

2020 ◽  
Author(s):  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
Xian Wu ◽  
Yong Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Leaf Spot ◽  
Guizhou Province ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Rna Sequences ◽  
Lasiodiplodia Theobromae ◽  
Tea Leaf

Lasiodiplodia theobromae (Pat.) Griffon & Maubl. is a phytopathogenic fungus, which can cause many different diseases on different crops. The pathogen can cause leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in tea plantations in Guizhou Province, China. Although the genome sequence of L. theobromae has been published, no data on the transcriptome or small RNA sequences of L. theobromae under in vitro conditions and the course of infection of tea leaf are available. Here, we report the high-quality transcriptome and small RNA sequences of L. theobromae under in vitro conditions and the course of infection of tea leaf using the platform of Illumina HiSeq. This comprehensive expression profiling of the fungal pathogen will provide a valuable resource for future research on trait-specific genes of the pathogen, host-pathogen interactions and on disease resistance in the host.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

scholarly journals Functional Annotation of circRNAs in Tea Leaves after Infection by the Tea Leaf Spot Pathogen, Lasiodiplodia theobromae

2021 ◽  
Author(s):  
Yuanyou Yang ◽  
Xinyue Jiang ◽  
Jiayan Shi ◽  
Yu Wang ◽  
Honglin Huang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Protein Kinase ◽  
Leaf Spot ◽  
Functional Annotation ◽  
Wrky Transcription Factor ◽  
Differentially Expressed ◽  
Tea Leaves ◽  
Lasiodiplodia Theobromae ◽  
Host Pathogen ◽  
Tea Leaf

Tea leaf spot, caused by Lasiodiplodia theobromae, is an important disease that can seriously decrease the production and quality of tea (Camellia sinensis [L.] Kuntze) leaves. The analysis of circular RNA (circRNA) in tea leaves after infection by the pathogen could improve understanding about the mechanism of host-pathogen interactions. In this study, high-performance sequencing of circRNA from C. sinensis Fuding-dabaicha leaves that had been infected with L. theobromae was conducted using the Illumina HiSeq 4000 platform. A total of 192 and 153 differentially-expressed circRNAs from tea leaves were significantly up- and down-regulated, respectively, after infection with L. theobromae. A GO analysis indicated that the differentially expressed circRNA-hosting-genes for DNA binding were significantly enriched. The genes with significantly differential expressions that were annotated in the specified database (S genes) were Sigma factor E isoform 1, Triacylglycerol lipase SDP1, DNA-directed RNA polymerase III subunit 2, WRKY transcription factor WRKY24, and regulator of nonsense transcripts 1 homolog. A KEGG analysis indicated that the significantly enriched circRNA-hosting-genes involved in the plant-pathogen interaction pathway were Calmodulin-domain protein kinase 5 isoform 1, probable WRKY transcription factor 33, U-box domain-containing protein 35, probable inactive receptor-like protein kinase At3g56050, WRKY transcription factor WRKY24, mitogen-activated protein kinase kinase kinase YODA, SGT1, and protein DGS1, etc. Functional annotation of circRNAs in tea leaves infected by L. theobromae will provide a valuable resource for future research on host-pathogen interactions.

scholarly journals Identification and integrated analysis of CircRNA and miRNA of Radiation-Induced lung injury in a mice model

2020 ◽  
Author(s):  
Xi Yang ◽  
Yida Li ◽  
Liqing Zou ◽  
Li Chu ◽  
Luxi Ye ◽  
...  
Keyword(s):  
Lung Injury ◽  
Signaling Pathway ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Normal Lung ◽  
Future Research ◽  
Circular Rnas ◽  
Integrated Analysis ◽  
Mice Model ◽  
Radiation Induced

Abstract Radiation-induced lung injury (RILI) is a main threat to patients received thoracic radiotherapy, it is of great importance to understand the molecular mechanism of RILI. Circular RNAs (CircRNAs) have been found to act as the regulator of multiple biological processes and circRNA-miRNA-mRNA axis could play an important role in signaling pathway of many human diseases including radiation injury, here, we first investigate the circRNA and miRNA of radiation-induced lung injury in a mice model. The mice received 12 Gy thoracic irradiation and the irradiated lung tissues at 48 hours after irradiation were analyzed by RNA Sequencing (RNA-seq) technique compared with normal lung tissues. We identified 21 significantly up-regulated while significantly 33 down-regulated miRNAs. Among 27 differentially expressed circRNAs, 10 were down-regulated and 17 were up-regulated. We then performed circRNAs GO analysis of the target mRNAs of these significantly differently expressed circRNAs. These differentially expressed miRNAs took part in series of cellular processes such as positive regulation of alpha-beta T cell proliferation, interstitial matrix, collagen fibril organization, chemokine receptor activity, cellular defense response, and B cell receptor signaling pathway. Through this study, we found that immune-related molecular pathways play an important role in the early response after radiotherapy. In the future, research on the target mechanism and early intervention of circRNAs with associated miRNAs will benefit the treatment of RILI.

scholarly journals Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

2021 ◽  
Vol 11 ◽  
Author(s):  
Min Cao ◽  
Xu Yan ◽  
Baofeng Su ◽  
Ning Yang ◽  
Qiang Fu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Signaling Pathway ◽  
Regulatory Networks ◽  
Target Genes ◽  
Differentially Expressed ◽  
Edwardsiella Tarda ◽  
Circular Rnas ◽  
Integrated Analysis ◽  
Apoptosis Pathway ◽  
Sebastes Schlegelii

Sebastes schlegelii, an important aquaculture species, has been widely cultured in East Asian countries. With the increase in the cultivation scale, various diseases have become major threats to the industry. Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions in the interactions between pathogens and their hosts. However, little is known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in the process of preventing pathogen infection in the intestine in teleosts. In this study, we aimed to uncover the global landscape of mRNAs, circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda infection at different time points (0, 2, 6, 12, and 24 h) and to construct regulatory networks for exploring the immune regulatory mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87 circRNAs, and 79 miRNAs were differentially expressed. The differentially expressed RNAs were quantitatively validated using qRT-PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the differentially expressed mRNA genes and the target genes of ncRNAs were related to immune signaling pathways, such as the NF-κB signal pathway, pathogen recognition receptors related to signaling pathways (Toll-like receptors and Nod-like receptors), and the chemokine signaling pathway. Based on these differentially expressed genes, 624 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA interaction networks. In a novel_circ_0004195/novel-530/IκB interaction network, novel_530 was upregulated, while its two targets, novel_circ_0004195 and IκB, were downregulated after E. tarda infection. In addition, two circRNA-miRNA-mRNA networks related to apoptosis (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1 receptor type 2) were also identified in our study. We thus speculated that the downstream NF-κB signaling pathway, p53 signaling pathway, and apoptosis pathway might play vital roles in the immune response in the intestine of S. schlegelii. This study revealed a landscape of RNAs in the intestine of S. schlegelii during E. tarda infection and provided clues for further study on the immune mechanisms and signaling networks based on the circRNA-miRNA-mRNA axis in S. schlegelii.

Non-coding RNA Associated Competitive Endogenous RNA Regulatory Network: Novel Therapeutic Approach in Liver Fibrosis

2019 ◽  
Vol 19 (5) ◽  
pp. 305-317 ◽  
Author(s):  
Farooq Riaz ◽  
Dongmin Li
Keyword(s):  
Liver Fibrosis ◽  
Target Genes ◽  
Signaling Cascades ◽  
Circular Rnas ◽  
Pathological Feature ◽  
Non Coding Rna ◽  
Overwhelming Evidence ◽  
Competing Endogenous Rnas ◽  
Non Coding Rnas ◽  
Competitive Endogenous Rna

Liver fibrosis or scarring is the most common pathological feature caused by chronic liver injury, and is widely considered one of the primary causes of morbidity and mortality. It is primarily characterised by hepatic stellate cells (HSC) activation and excessive extracellular matrix (ECM) protein deposition. Overwhelming evidence suggests that the dysregulation of several noncoding RNAs (ncRNAs), mainly long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs) contributes to the activation of HSC and progression of liver fibrosis. These ncRNAs not only bind to their target genes for the development and regression of liver fibrosis but also act as competing endogenous RNAs (ceRNAs) by sponging with miRNAs to form signaling cascades. Among these signaling cascades, lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA are critical modulators for the initiation, progression, and regression of liver fibrosis. Thus, targeting these interacting ncRNA cascades can serve as a novel and potential therapeutic target for inhibition of HSC activation and prevention and regression of liver fibrosis.

scholarly journals The emerging roles of non-coding competing endogenous RNA in hepatocellular carcinoma

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Gang Xu ◽  
Wei-Yu Xu ◽  
Yao Xiao ◽  
Bao Jin ◽  
Shun-Da Du ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Epithelial Mesenchymal Transition ◽  
Future Research ◽  
Circular Rnas ◽  
Transcriptional Level ◽  
Biological Processes ◽  
Diagnostic Biomarkers ◽  
Mesenchymal Transition ◽  
Regulatory Interactions ◽  
Competing Endogenous Rnas

Abstract Accumulating evidence has emerged revealing that noncoding RNAs (ncRNAs) play essential roles in the occurrence and development of hepatocellular carcinoma (HCC). However, the complicated regulatory interactions among various ncRNAs in the development of HCC are not entirely understood. The newly discovered mechanism of competing endogenous RNAs (ceRNAs) uncovered regulatory interactions among different varieties of RNAs. In recent years, a growing number of studies have suggested that ncRNAs, including long ncRNAs, circular RNAs and pseudogenes, play major roles in the biological functions of the ceRNA network in HCC. These ncRNAs can share microRNA response elements to affect microRNA affinity with target RNAs, thus regulating gene expression at the transcriptional level and both physiological and pathological processes. The ncRNAs that function as ceRNAs are involved in diverse biological processes in HCC cells, such as tumor cell proliferation, epithelial-mesenchymal transition, invasion, metastasis and chemoresistance. Based on these findings, ncRNAs that act as ceRNAs may be promising candidates for clinical diagnosis and treatments. In this review, we discuss the mechanisms and research methods of ceRNA networks. We also reviewed the recent advances in studying the roles of ncRNAs as ceRNAs in HCC and highlight possible directions and possibilities of ceRNAs as diagnostic biomarkers or therapeutic targets. Finally, the limitations, gaps in knowledge and opportunities for future research are also discussed.

scholarly journals Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic Skin

2021 ◽  
Vol 22 (10) ◽  
pp. 5182
Author(s):  
Xiaoxin Liu ◽  
Jacqueline Frost ◽  
Anne Bowcock ◽  
Weixiong Zhang
Keyword(s):  
Noncoding Rna ◽  
Circular Rnas ◽  
Psoriatic Skin ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Competing Endogenous Rnas ◽  
Intergenic Regions ◽  
Comprehensive Search ◽  
Novel Method ◽  
Exon Junctions

(1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 skin biopsy samples to comprehensively identify circRNAs of all types, i.e., canonical circRNAs from the intron-exon junctions of mRNAs and interior circRNAs (i-circRNAs) from the interior regions of exons, introns, and intergenic regions. Selected circRNAs were experimentally validated by qRT-PCR and Sanger sequencing. CircRNAs with abundant and differential expression were identified and their putative function as competing endogenous RNAs (ceRNAs) was analyzed by an integrated analysis of circRNAs, microRNAs, and mRNAs. (3) Results: With a comprehensive search using no information of splicing signals, we systematically identified 179 highly abundant circRNAs in psoriatic skin. Many of these were reported for the first time and many were differentially expressed in involved versus normal or uninvolved skin. Validation based on three additional RNA-seq datasets confirmed most of the identified circRNAs in psoriatic skin. Experimental analyses confirmed the expression of the well-known circRNA CDR1as, a canonical circRNA, and a novel i-circRNA in psoriasis. We also identified many circRNAs that may act as ceRNAs to regulate the expression of mRNA genes in psoriasis-related signaling pathways in psoriasis. (4) Conclusions: The result of the study suggested that circRNAs are abundant in psoriatic skin, have distinct characteristics, and contribute to psoriatic pathogenesis.

scholarly journals Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae

2021 ◽  
Author(s):  
Huishan Liu ◽  
Chinedu Charles Nwafor ◽  
Yinglan Piao ◽  
Xiaonan Li ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Brassica Rapa ◽  
Target Genes ◽  
Zinc Finger Protein ◽  
Plasmodiophora Brassicae ◽  
Resistance Mechanisms ◽  
Circular Rnas ◽  
Clubroot Disease ◽  
Clubroot Resistance ◽  
Competing Endogenous Rnas

Abstract BackgroundPlasmodiophora brassicae is a soil-borne pathogen that attacks the roots of cruciferous plants, causing clubroot disease. CircRNAs are non-coding RNAs widely exist in plant and animal species which can acting as “microRNA (miRNA) sponges” and “competing endogenous RNAs (ceRNAs)”. Knowledge of circRNAs has been updated continuously and rapidly. However, the information about circRNAs in the regulation of clubroot-disease resistance is limited in Brassica rapa. ResultsHere, the Chinese cabbage (BJN 222) containing clubroot resistance gene (CRa) resistant to the Pb4 was susceptible to the PbE of P. brassicae. To investigate the mechanism of cicRNAs responsible for clubroot-disease resistance in Brassica rapa, the circRNA-seq was performed roots of BJN 222 at 0 d, 8 d, and 23 d after inoculated with Pb4 and PbE. A total of 1636 circRNAs were detected distributed on 10 chromosomes. Furthermore, total 231 differentially expressed circRNAs between groups were screened. Parental genes of circRNAs functions analysis results indicated that the expression of circRNAs was affected not only by inoculation time but also by the pathogenicity of P. brassicae. However, the “Phenylalanine, tyrosine, and tryptophan biosynthesis” pathway was significant enriched between the two pathotypes at different inoculation times. All the expression of target genes annotated with “receptor-like protein kinase,” “zinc finger protein,” “LRR-repeat protein,” and “hormone-related” identified from the circRNA-miRNA-mRNA network were analyzed. 5 target genes were consistent with the expression pattern of novel_circ_000495 at 8 dpi, but only Bra026508 was significantly up-regulated. ConclusionThe up-regulated novel_circ_000495 might suppressed the expression of miR5656-y, leading to the up-regulation of Bra026508. Our results provided new insights to clubroot resistance mechanisms of B.rapa and laid a foundation for further research on the function of circRNAs responsible for the pathogen infection.

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