Expression analysis of argonaute, Dicer-like, and RNA-dependent RNA polymerase genes in cucumber (Cucumis sativus L.) in response to abiotic stress

Gan, Defang; Zhan, Mengdan; Yang, Feng; Zhang, Qi-Qi; Hu, Keling; Xu, Wenjuan; Lü, Qin; Zhang, Ling; Liang, Dandi

doi:10.1007/s12041-017-0758-y

Cited by 38 publications

(22 citation statements)

References 49 publications

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“…Global climate change threatens crop yield by imposing ambient pressures such as cold, drought, salinity, heat and other abiotic and biotic stresses [1]. Numerous studies indicate that small RNAs (sRNAs) have important roles in gene expression regulation during the abiotic and biotic stresses in all plants [2–6].…”

Section: Introductionmentioning

confidence: 99%

Expression analysis of Argonaute genes in maize (Zea mays L.) in response to abiotic stress

et al. 2019

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Background Argonaute (AGO) protein is a kind of RNA binding protein that plays an integral role in the gene-silencing pathways guided by small RNAs. But there are few studies about the regulation of AGO genes responded to diverse abiotic stress in maize. Results In this study, we analyzed the expression of seventeen ZmAGO genes under heat, cold, salinity, drought and ABA treatments using quantitative PCR (qPCR). All ZmAGOs showed differential expression modes under various abiotic stress treatments. Two ZmAGOs ( ZmAGO1a and ZmAGO5d ) and other fifteen ZmAGOs exhibited specific up-regulation in response to heat separately. Several ZmAGO genes are very sensitive to cold stress, but many ZmAGO genes are slow to respond to NaCl treatment. Nine ZmAGO genes ( ZmAGO1f , ZmAGO2b , ZmAGO4 , ZmAGO5a/b/c , ZmAGO7 , ZmAGO9 and ZmAGO18a/b ) presented definite up-regulation in response to drought, which were similar to the pattern of gene regulation under abscisic acid (ABA) treatment. Conclusions Various ZmAGO genes respond to different abiotic stress treatments. These results provide fundamental information and insights for the further study on the role of abiotic stress resistance genes in maize and provide basis for further study on the function of AGO genes in response to abiotic stress in maize. Electronic supplementary material The online version of this article (10.1186/s41065-019-0102-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Expression analysis of Argonaute genes in maize (Zea mays L.) in response to abiotic stress

et al. 2019

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“…The TFs MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP families might play significant role in regulating RNAi genes. Particularly those of ERF, NAC, WRKY and bZIP families, which are the top four families those contained 29,20,20 and 10 TFs and accounted 57.66% of the total identified TFs ( Supplementary Table S3). This finding indicated that those TFs could be important in regulating RNAi genes.…”

Section: Regulatory Relationship Between Tfs and Rnai Genesmentioning

confidence: 99%

“…The EST mining results from the PlantGDB database indicated that the RNAi genes of C. sinensis expressed in multiple important tissue and organs. However, the expression evidence of the RNAi genes in several species has been reported which showed that the RNAi genes have expression in leaf, root, flower, seeds and in others tissue [13,[23][24][25][26][27][28][29][30]73].…”

Section: In Silico Expressed Sequence Tag (Est) Analysismentioning

confidence: 99%

“…The member of these RNAi gene families has been identified in many plants species (such as Arabidopsis [23], rice [13], maize [24], tomato [25], tobacco [26], foxtail millet [27], and grapevine [28], cucumber [29], pepper [30]). In Arabidopsis, AtDCL1, AtDCL3 and AtAGO4 influenced the RNA-directed DNA methylation of the FWA transgene linkage to the histone H3 lysine 9 (H3K9) methylation [31,32].…”

Section: Introductionmentioning

confidence: 99%

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In SilicoIdentification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (Citrus sinensis L)

Rahman

et al. 2020

Preprint

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RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families. However, the genes of these three RNAi families are largely unknown yet in sweet orange (Citrus sinensis), though it is an economically important fruit plant all over the world. Therefore, a comprehensive investigation for genome-wide identification, characterization and diversity analysis of RNA silencing genes in C. sinensis was conducted and identified 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi genes. To characterize and validate the predicted genes of RNAi families, various bioinformatics analysis was conducted. Phylogenetic analysis clustered the predicted CsDCLs, CsAGOs and CsRDRs genes into four, six and four subgroups with the relevant genes of Arabidopsis respectively. The domain and motif composition analysis, the gene structure for all three-gene families exhibited almost homogeneity within the same group members while showed significant differences in between groups. The GO enrichment analysis results clearly indicated that the predicted genes have direct involvement into the RNAi process as expected in C. sinensis. Moreover, Cis-regulatory elements and regulatory transcription factor analysis of the reported RNAi genes demonstrated the diverse connection to the huge biological functions and regulatory pathways. The expressed sequence tag (EST) analysis showed that these genes are highly expressed in fruit and leaves which indicate that these reported genes have great involvement in C. sinensis food, flowering and fruit production. The expression analysis of the reported RNAi genes might be more useful to explore the most effectiveRNAi genes in C. sinensis for further biotechnological application.

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“…Argonaute (Ago) proteins can mediate target silencing by translational repression and de-adenylation coupled with mRNA decay, which has an impact on diverse biological processes ( Sasaki and Tomari, 2012 ). Many Agos that respond to chilling stress (CS) are found in various plant species, such rice ( Kapoor et al, 2008 ), wheat ( Meng et al, 2013 ), and cucumber ( Gan et al, 2017 ). The identification of VvAgo1 in response to CS ( Bao et al, 2013 ) suggests that fungal Agos are responsible for chilling stress-response similar to plant Agos.…”

Section: Introductionmentioning

confidence: 99%

Chilling Stress Triggers VvAgo1-Mediated miRNA-Like RNA Biogenesis in Volvariella volvacea

et al. 2020

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In Volvariella volvacea, an important species of edible mushroom, cryogenic autolysis is a typical phenomenon that occurs during abnormal metabolism. Analysis of gene expression profiling and qPCR showed that chilling stress (CS) significantly and continuously upregulated only one type of Argonaute in V. volvacea, i.e., VvAgo1. Structural and evolutionary analysis revealed that VvAgo1 belongs to the Ago-like family, and its evolution has involved gene duplication, subsequent gene loss, and purifying selection. Analysis of its interaction network and expression suggested that CS triggers VvAgo1-mediated miRNA-like RNA (milRNA) biogenesis in V. volvacea V23 but not in VH3 (a composite mutant strain from V23 with improved CS resistance). Small RNA sequencing and qPCR analysis confirmed that CS triggered the increased milRNA expression in V23 and not in VH3. The predicted target genes of the increased milRNAs were enriched in several pathways, such as signal transduction and ubiquitination. Heatmap analysis showed that CS altered the expression profile of milRNAs with their target genes related to signal transduction and ubiquitination in V23. Combined analysis of transcriptome and proteome data confirmed that most of the target genes of the increased milRNAs were not translated into proteins. Our observations indicate that CS might trigger VvAgo1-mediated RNAi to facilitate the cryogenic autolysis of V. volvacea.

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Expression analysis of argonaute, Dicer-like, and RNA-dependent RNA polymerase genes in cucumber (Cucumis sativus L.) in response to abiotic stress

Cited by 38 publications

References 49 publications

Expression analysis of Argonaute genes in maize (Zea mays L.) in response to abiotic stress

Expression analysis of Argonaute genes in maize (Zea mays L.) in response to abiotic stress

In SilicoIdentification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (Citrus sinensis L)

Chilling Stress Triggers VvAgo1-Mediated miRNA-Like RNA Biogenesis in Volvariella volvacea

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