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

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.

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

Phytopathology ◽

10.1094/phyto-05-21-0184-a ◽

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.

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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 ◽

10.1094/pdis-06-21-1324-a ◽

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.

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Sequencing and functional analysis of mRNAs and lncRNAs from tea (Camellia sinensis) leaves during infection by the fungal pathogen, Lasiodiplodia theobromae

PhytoFrontiers™ ◽

10.1094/phytofr-03-21-0020-a ◽

2021 ◽

Author(s):

Dongxue Li ◽

Shilong Jiang ◽

Xiaodong Wen ◽

Xingchen Song ◽

Yuanyou Yang ◽

...

Keyword(s):

Functional Analysis ◽

Association Studies ◽

Glycosyl Hydrolase ◽

Control Measures ◽

Differentially Expressed ◽

Effective Control ◽

Future Research ◽

Tea Leaves ◽

Illumina Hiseq ◽

Lasiodiplodia Theobromae

Due to the absence of effective control measures, tea leaf spot, caused by Lasiodiplodia theobromae, can seriously reduce the production and quality of tea leaves. Analysis of the relationship between messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) of tea could help to prevent and control the disease. In this current study, high-performance sequencing of mRNA and lncRNA from tea leaves during infection by L. theobromae was conducted using the Illumina HiSeq 4000 platform. Of the differentially expressed mRNAs, 2,503 or 5,278 were significantly up or down regulated, respectively, in challenged leaves, relative to unchallenged leaves. Differentially expressed lncRNAs were also analyzed at the level of genes for the above two treatments. The number of significantly up- or down-regulated lncRNAs were 3,403 or 1,477, respectively. Functional analysis of mRNA revealed that L. theobromae challenge can induce the up regulation of the genes of Seven transmembrane MLO family protein -3, -6, -11, Major allergen Pru ar 1, etc. A total of 176 differentially expressed lncRNAs occurred in response to L. theobromae challenge as a result of cis regulation, with 146 differentially expressed mRNAs. At the biological process of defense response, Glycosyl hydrolase 9A1 gene was cis regulated by the differentially expressed lncRNA. The expression profiling and association studies of the tea host infected by L. theobromae will provide a resource for future research into host–pathogen interactions and disease resistance.

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Whole Genome Sequences of the Tea Leaf Spot Pathogen Didymella segeticola

Phytopathology ◽

10.1094/phyto-02-19-0050-a ◽

2019 ◽

Vol 109 (10) ◽

pp. 1676-1678 ◽

Cited By ~ 1

Author(s):

Yafeng Ren ◽

Dongxue Li ◽

Xiaozhen Zhao ◽

Yong Wang ◽

Xingtao Bao ◽

...

Keyword(s):

Leaf Spot ◽

Guizhou Province ◽

Whole Genome Sequence ◽

Future Research ◽

Whole Genome ◽

Plant Host ◽

Illumina Hiseq ◽

Leaf Production ◽

Clusters Of Orthologous Groups ◽

Tea Leaf

The fungal pathogen Didymella segeticola (basionym Phoma segeticola) causes leaf spot on tea (Camellia sinensis), which leads to a loss in tea leaf production in Guizhou Province, China. D. segeticola isolate GZSQ-4 was sequenced using Illumina HiSeq and Pacific Biosciences (PacBio) RS technologies, and then assembled to approximately 33.4 Mbp with a scaffold N50 value of approximately 2.3 Mbp. In total, 10,893 genes were predicted using the Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. The whole-genome sequence of D. segeticola will provide a resource for future research on host−pathogen interactions, determination of trait-specific genes, pathogen evolution, and plant−host adaptation mechanisms.

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

Phytopathology ◽

10.1094/phyto-07-20-0297-a ◽

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.

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Bioinformatics Analysis of Key Genes and circRNA-miRNA-mRNA Regulatory Network in Gastric Cancer

BioMed Research International ◽

10.1155/2020/2862701 ◽

2020 ◽

Vol 2020 ◽

pp. 1-16 ◽

Cited By ~ 1

Author(s):

Yiting Tian ◽

Yang Xing ◽

Zheng Zhang ◽

Rui Peng ◽

Luyu Zhang ◽

...

Keyword(s):

Gastric Cancer ◽

Extracellular Matrix ◽

Expression Profiles ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Receptor Interaction ◽

Future Research ◽

Circular Rnas ◽

Ppi Network ◽

Protein Protein Interaction

Gastric cancer (GC) is one of the most common malignancies in the world, with morbidity and mortality ranking second among all cancers. Accumulating evidences indicate that circular RNAs (circRNAs) are closely correlated with tumorigenesis. However, the mechanisms of circRNAs still remain unclear. This study is aimed at determining hub genes and circRNAs and analyzing their potential biological functions in GC. Expression profiles of mRNAs and circRNAs were downloaded from the Gene Expression Omnibus (GEO) data sets of GC and paracancer tissues. Differentially expressed genes (DEGs) and differentially expressed circRNAs (DE-circRNAs) were identified. The target miRNAs of DE-circRNAs and the bidirectional interaction between target miRNAs and DEGs were predicted. Functional analysis was performed, and the protein-protein interaction (PPI) network and the circRNA-miRNA-mRNA network were established. A total of 456 DEGs and 2 DE-circRNAs were identified with 3 mRNA expression profiles and 2 circRNA expression profiles. GO analysis indicated that DEGs were mainly enriched in extracellular matrix and cell adhesion, and KEGG confirmed that DEGs were mainly associated with focal adhesion, the PI3K-Akt signaling pathway, extracellular matrix- (ECM)- receptor interaction, and gastric acid secretion. 15 hub DEGs (BGN, COL1A1, COL1A2, FBN1, FN1, SPARC, SPP1, TIMP1, UBE2C, CCNB1, CD44, CXCL8, COL3A1, COL5A2, and THBS1) were identified from the PPI network. Furthermore, the survival analysis indicate that GC patients with a high expression of the following 9 hub DEGs, namely, BGN, COL1A1, COL1A2, FBN1, FN1, SPARC, SPP1, TIMP1, and UBE2C, had significantly worse overall survival. The circRNA-miRNA-mRNA network was constructed based on 1 circRNA, 15 miRNAs, and 45 DEGs. In addition, the 45 DEGs included 5 hub DEGs. These results suggested that hub DEGs and circRNAs could be implicated in the pathogenesis and development of GC. Our findings provide novel evidence on the circRNA-miRNA-mRNA network and lay the foundation for future research of circRNAs in GC.

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

10.21203/rs.3.rs-56653/v1 ◽

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.

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Integrated mRNA and Small RNA Sequencing for Analyzing Leaf Spot Pathogen Didymella segeticola and Its Host, Tea (Camellia sinensis), During Infection

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-07-20-0207-a ◽

2020 ◽

pp. MPMI-07-20-0207

Author(s):

Rui Yang ◽

Silong Jiang ◽

Dongxue Li ◽

Qiaoxiu Yin ◽

Xian Wu ◽

...

Keyword(s):

Camellia Sinensis ◽

Leaf Spot ◽

Resistance Mechanisms ◽

Guizhou Province ◽

Future Research ◽

Small Rna Sequencing ◽

Illumina Hiseq ◽

Tea Plants ◽

Open Access Article

Leaf spot on tea plants (Camellia sinensis [L.] Kuntze), caused by the fungus Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola), negatively affects the productivity and quality of tea leaves in Guizhou Province, China. Although the genome sequence of D. segeticola has been published, no data on the transcriptome or microRNAs (miRNAs) of the pathogen or host during infection are available. Here, we report on the high-quality transcriptome and miRNA sequences of both D. segeticola and tea during infection, using the Illumina HiSeq 4000 or HiSeq 2500 platforms. Comprehensive expression profiling of the fungal pathogen and its host will provide a resource for future research into trait-specific genes of the pathogen and the host as well as on host-pathogen interactions and on disease resistance mechanisms. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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The circular RNA circSlc7a11 promotes bone cancer pain pathogenesis in rats by modulating LLC-WRC 256 cell proliferation and apoptosis

Molecular and Cellular Biochemistry ◽

10.1007/s11010-020-04020-1 ◽

2021 ◽

Author(s):

Han-Wen Chen ◽

Xiao-Xia Zhang ◽

Zhu-Ding Peng ◽

Zu-Min Xing ◽

Yi-Wen Zhang ◽

...

Keyword(s):

Cell Proliferation ◽

Cancer Pain ◽

Expression Profiles ◽

Bone Cancer ◽

Circular Rna ◽

Differentially Expressed ◽

Bone Cancer Pain ◽

Circular Rnas ◽

Altered Expression ◽

Proliferation And Apoptosis

AbstractTreatment of bone cancer pain (BCP) caused by bone metastasis in advanced cancers remains a challenge in clinical oncology, and the underlying mechanisms of BCP are poorly understood. This study aimed to investigate the pathogenic roles of circular RNAs (circRNAs) in regulating cancer cell proliferation and BCP development. Eight differentially expressed circRNAs in the rat spinal cord were validated by agarose gel electrophoresis and Sanger sequencing. Expression of circRNAs and mRNAs was detected by quantitative RT-PCR. MTS assay and flow cytometry were performed to analyze cell proliferation and apoptosis, respectively. Differentially expressed mRNA profiles were characterized by deep RNA sequencing, hierarchical clustering, and functional categorization. The interactions among circRNAs, microRNAs (miRNAs), and mRNAs were predicted using TargetScan. Additionally, western blot was performed to determine the protein levels of Pax8, Isg15, and Cxcl10. Multiple circRNAs were differentially expressed in the spinal cords of BCP model rats; of these, circSlc7a11 showed the greatest increase in expression. The overexpression of circSlc7a11 significantly promoted cell proliferation and repressed apoptosis of LLC-WRC 256 and UMR-106 cells, whereas circSlc7a11 silencing produced the opposite effects. Altered expression of circSlc7a11 also induced substantial changes in the mRNA expression profiles of LLC-WRC 256 cells; these changes were linked to multiple apoptotic processes and signaling pathways, such as the chemokine signaling pathway, and formed a complex circRNA/miRNA/mRNA network. Additionally, Pax8, Isg15, and Cxc110 protein level in LLC-WRC 256 cells was consistent with the mRNA results. The circRNA circSlc7a11 regulates rat BCP development by modulating LLC-WRC 256 cell proliferation and apoptosis through multiple-signaling mechanisms.

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