Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis

Pantaleo, Vitantonio; Szittya, György; Moxon, Simon; Miozzi, Laura; Moulton, Vincent; Dalmay, Tamás; Burgyán, József

doi:10.1111/j.1365-313x.2010.04208.x

Cited by 91 publications

(123 citation statements)

References 62 publications

(95 reference statements)

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“…In this study, we generated two sRNA libraries from the main stem of P. beijingensis treated and untreated with Dothiorella gregaria pathogen. We obtained almost 18 million reads of 18-30 nt per library, more than previous reports on single sRNA libraries generated through deep sequencing (Klevebring et al 2009;Kwak et al 2009;Pantaleo et al 2010;Zhang et al 2009;Zhao et al 2010). We thus believe that we have generated a relatively complete sRNA library and that we could identify more novel miRNAs through further analysis of these sRNAs.…”

Section: Discussionmentioning

confidence: 74%

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

Chen

Ren

Zhang

et al. 2011

Planta

102

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MicroRNAs (miRNAs) are small RNAs, generally of 20-23 nt, that down-regulate target gene expression during development, differentiation, growth, and metabolism. In Populus, extensive studies of miRNAs involved in cold, heat, dehydration, salinity, and mechanical stresses have been performed; however, there are few reports profiling the miRNA expression patterns during pathogen stress. We obtained almost 38 million raw reads through Solexa sequencing of two libraries from Populus inoculated and uninoculated with canker disease pathogen. Sequence analyses identified 74 conserved miRNA sequences belonging to 37 miRNA families from 154 loci in the Populus genome and 27 novel miRNA sequences from 35 loci, including their complementary miRNA* strands. Intriguingly, the miRNA* of three conserved miRNAs were more abundant than their corresponding miRNAs. The overall expression levels of conserved miRNAs increased when subjected to pathogen stress, and expression levels of 33 miRNA sequences markedly changed. The expression trends determined by sequencing and by qRT-PCR were similar. Finally, nine target genes for three conserved miRNAs and 63 target genes for novel miRNAs were predicted using computational analysis, and their functions were annotated. Deep sequencing provides an opportunity to identify pathogen-regulated miRNAs in trees, which will help in understanding the regulatory mechanisms of plant defense responses during pathogen infection.

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Section: Discussionmentioning

confidence: 74%

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

Chen

Ren

Zhang

et al. 2011

Planta

102

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“…Although most viroids do not induce visible symptoms in infected grapevines, viroid interference with the regulation of host gene expression and metabolic pathways, and their influence on the quality and/or quantity of the final crop, have not been thoroughly investigated. The availability of virus-and viroidfree grapevine cultivars, made possible by somatic embryogenesis, opens up new and fascinating perspectives that have been further enhanced by the publication of the complete grapevine genome sequence (Jaillon et al 2007;Velasco et al 2007) and by the recent application of genome-wide technologies to grapevines (Navarro et al 2009;Mica et al 2009;Pantaleo et al 2010). Altogether, these factors contribute to making grapevines one of the best available experimental models for exploring the molecular mechanisms underlying plant-viroid interactions by high-throughput technologies.…”

Section: Discussionmentioning

confidence: 96%

Somatic embryogenesis efficiently eliminates viroid infections from grapevines

Gambino¹,

Navarro²,

Vallania³

et al. 2011

Eur J Plant Pathol

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Indirect somatic embryogenesis is effective at eliminating the most important viruses affecting grapevines. Accordingly, this technique was tested as a method for eradicating two widespread viroids, Grapevine yellow speckle viroid 1 (GYSVd-1) and Hop stunt viroid (HSVd), from four grapevine cultivars. Both viroids were detected by RT-PCR in grapevine floral explants used for initiating embryogenic cultures, as well as in undifferentiated cells of embryogenic and non-embryogenic calli from anthers and ovaries. In contrast, somatic embryos differentiated from these infected calli were viroid-free, and viroids were not detected in embryo-derived plantlets even 3 years after their transfer to greenhouse conditions. A wider spatial distribution of HSVd than GYSVd-1 within proliferating calli was revealed by in situ hybridization, whereas no hybridization signal was detected in the somatic embryos. In addition, GYSVd-1 and HSVd were localised in the nucleus of infected cells, conclusively showing the nuclear accumulation of representative members of Apscaviroid and Hostuviroid genera, which has been only an assumption so far. Somatic embryogenesis was compared to in vitro thermotherapy, a technique routinely used for virus eradication. After thermotherapy, HSVd and GYSVd-1 were detected in all in vitro plantlets of the cultivar Roussan, and in all lines analysed after 3 years of culture in greenhouse. The high efficiency with which somatic embryogenesis may eliminate viroids and viruses from several infected grapevine cultivars, should allow the availability of virus-and viroid-free material, which would be useful not only for sanitary selection but also for basic research on plant-virus and plant-viroid interactions in grapevine.

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“…Further efforts are required including profiling the differential expression patterns under variable conditions and functionally validating the precise regulatory roles of these Pb-responsive miRNAs in radish responses to Pb stress. miRNA-Mediated Regulatory Networks Responsive to Pb Stress miRNAs were shown to be involved in the post-transcriptional regulation of gene expression by mRNA degradation (Pantaleo et al 2010). Currently, high-throughput degradome sequencing is a valuable and efficient approach to validate and characterize target genes of miRNAs (German et al 2008;Shamimuzzaman and Vodkin 2012).…”

Section: Identification Of Pb-responsive Mirnas By Solexa Sequencing mentioning

confidence: 99%

“…This type of analysis, commonly known as 'Degradome' analysis, provides short sequencing reads that match sites in mRNAs that are prone to degradation. By now, this high-throughput technology of sRNAs and degradome analysis has been extensively applied in a number of plant species for miRNA identification, quantification and target gene validation, such as rice (Li et al 2010b;Ma et al 2013;Zhou et al 2010), maize , soybean (Shamimuzzaman and Vodkin 2012;Song et al 2011;Xu et al 2013a), Brassica juncea , Populus trichocarpa (Shuai et al 2013), Medicago truncatula (Branscheid et al 2011;Zhou et al 2012), grapevine (Pantaleo et al 2010) and Populus euphratica (Li et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification of Radish (Raphanus sativus L.) miRNAs and Their Target Genes to Explore miRNA-Mediated Regulatory Networks in Lead (Pb) Stress Responses by High-Throughput Sequencing and Degradome Analysis

et al. 2014

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Increasing evidence has revealed that microRNA (miRNA)-mediated gene regulation plays a significant role in response to heavy metal stresses. However, there is little information available about the expression patterns or roles of miRNAs under lead toxicity stress in plants. The radish is an important root vegetable crop with a fleshy taproot as the edible part. It was of vital importance to investigate the response mechanisms and explore the regulatory network at the molecular level under the heavy metal stresses in radish. In the present study, using high-throughput sequencing and degradome analysis, a genome-wide identification of radish miRNA and their targets under the exposure of Pb stress was conducted. A total of 74 known and 173 potential novel miRNAs were successfully identified from two radish root libraries of one untreated control (CK) and one Pb-stressed (Pb500). Of these, 25 known and nine novel miRNAs were significantly differentially expressed and identified as Pbresponsive miRNAs. Degradome analysis revealed that 1,979 miRNA-mRNA target transcripts could potentially be cleaved. Gene Ontology (GO) analysis revealed that these target transcripts were predominately involved in the regulation of transcription, defense responses, and binding related terms. The identified target genes for Pb-responsive miRNAs were mainly involved in stress-related signal sensing and transduction, specific metal uptake and homeostasis mechanisms. Additionally, the expression patterns of 20 Pbresponsive miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). These results provide fundamental insights into the miRNA-mediated regulatory networks and molecular mechanisms underlying plant responsiveness to Pb stresses.

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Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis

Cited by 91 publications

References 62 publications

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

Genome-wide profiling of novel and conserved Populus microRNAs involved in pathogen stress response by deep sequencing

Somatic embryogenesis efficiently eliminates viroid infections from grapevines

Identification of Radish (Raphanus sativus L.) miRNAs and Their Target Genes to Explore miRNA-Mediated Regulatory Networks in Lead (Pb) Stress Responses by High-Throughput Sequencing and Degradome Analysis

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