Differential expression of miRNAs and associated gene targets in grapevine leafroll-associated virus 3-infected plants

Bester, Rachelle; Burger, Johan T.; Maree, Hans J.

doi:10.1007/s00705-016-3197-9

Cited by 19 publications

(10 citation statements)

References 49 publications

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“…The data related to all the novel miRNAs identified so far in grapevine were collected from 18 already published works ( Carra et al, 2009 ; Pantaleo et al, 2010 , 2016 ; Wang et al, 2011 , 2012 , 2014 ; Alabi et al, 2012 ; Singh et al, 2012 ; Han et al, 2014 , 2016 ; Belli Kullan et al, 2015 ; Sun et al, 2015 ; Paim Pinto et al, 2016 ; Bester et al, 2017a , b ; Pagliarani et al, 2017 ; Snyman et al, 2017 ; Zhao et al, 2017 ). Each novel miRNA was aligned using BLAST both against the known miRNAs deposited in miRBase ( Kozomara and Griffiths-Jones, 2014 ) and against all the novel miRNAs retrieved by the different studies above cited.…”

Section: Methodsmentioning

confidence: 99%

“…In the last few years, from the first report concerning the identification of novel miRNAs in grapevine ( Carra et al, 2009 ), several works have been published on this topic, and many conserved and putative novel miRNAs were identified. Different species from the Vitis genus were analyzed, the most studied being several cultivars of Vitis vinifera ( Carra et al, 2009 ; Pantaleo et al, 2010 , 2016 ; Alabi et al, 2012 ; Belli Kullan et al, 2015 ; Sun et al, 2015 ; Paim Pinto et al, 2016 ; Bester et al, 2017a , b ; Pagliarani et al, 2017 ; Snyman et al, 2017 ) and the “Summer Black” hybrid of V. vinifera × Vitis labrusca ( Wang et al, 2011 , 2014 ; Han et al, 2014 ; Zhao et al, 2017 ). In addition, some miRNAs derived from Vitis amurensis ( Wang et al, 2012 ) and from a powdery mildew-resistant accession of the wild Chinese Vitis pseudoreticulata Baihe-35-1 ( Han et al, 2016 ) were characterized as well.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, some miRNAs derived from Vitis amurensis ( Wang et al, 2012 ) and from a powdery mildew-resistant accession of the wild Chinese Vitis pseudoreticulata Baihe-35-1 ( Han et al, 2016 ) were characterized as well. Substantially, all grapevine tissues in several developmental stages ( Belli Kullan et al, 2015 ) and from plants subjected to biotic ( Alabi et al, 2012 ; Singh et al, 2012 ; Pantaleo et al, 2016 ; Bester et al, 2017a ; Snyman et al, 2017 ) or abiotic stresses were analyzed ( Sun et al, 2015 ; Pantaleo et al, 2016 ; Pagliarani et al, 2017 ). Nevertheless, in these studies, there is no uniformity in the classification of the identified novel miRNAs: hundreds of putative novel miRNAs were indicated in different ways, and often the same miRNA was named differently in different works.…”

Section: Introductionmentioning

confidence: 99%

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miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection

et al. 2018

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Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganize the high quantity of available data, we produced “miRVIT,” the first database of all novel grapevine miRNA candidates characterized so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome, and compared with all the novel and conserved miRNAs detected in grapevine. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected “Barbera” grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it.Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection

et al. 2018

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“…MicroRNAs (miRNAs) are approximately 20-25 nt long and are important post-transcriptional regulators that modulate gene expression by targeting mRNAs for translational repression or cleavage [10,11]. An increasing number of miRNAs have been identified and their sequences have been deposited in a publicly available database (http://www.mirbase.org/).…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

Cao

Zhai

Zhang

et al. 2018

Forests

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Paulownia witches' broom (PaWB), caused by phytoplasma, is an important disease of Paulownia. To further identify the key miRNAs associated with the formation of PaWB symptoms, miRNA and degradome sequencing were performed to explore important miRNAs-target regulation in healthy and diseased Paulownia tomentosa, Paulownia fortunei, and P. tomentosa × P. fortunei seedlings, and the corresponding diseased seedlings treated with 75 mg L −1 dimethyl sulfate. A total of 212, 111, and 197 differentially expressed miRNAs (DEMs) were obtained in P. tomentosa, P. fortunei, and P. tomentosa × P. fortunei, respectively. Degradome sequencing detected 559, 251, and 568 target genes of the DEMs in P. tomentosa, P. fortunei, and P. tomentosa × P. fortunei, respectively. The expression patterns of selected miRNAs and the target genes were verified be qRT-PCR. Through analysis of the expression level of the DEMs in this study, combined with the results in our previous studies, as well as with those reported in other phytoplasma-infected plants, we concluded that miR156 is an important miRNA related to witches' broom. According to the functions of the target genes of DEMs, we constructed a co-regulatory network of the DEMs-target genes interaction. These results will help to advance the understanding of the mechanism of PaWB.

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“…Several types of sRNA species have been identified and characterised in plants, and their involvement in biotic stress responses have been suggested. These include microRNAs (miRNAs) [ 4 – 8 ], phased-siRNAs (phasiRNAs) [ 9 – 12 ], natural-antisense transcript siRNAs (nat-siRNAs) [ 12 – 14 ], repeat-associated siRNAs (rasiRNAs) [ 7 ] and tRNA-derived RNA fragments (tRFs) [ 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection

Visser

Cook

Burger

et al. 2017

Virol J

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BackgroundSmall RNA (sRNA) associated gene regulation has been shown to play a significant role during plant-pathogen interaction. In commercial citrus orchards co-infection of Citrus tristeza virus (CTV) and viroids occur naturally.MethodsA next-generation sequencing-based approach was used to study the sRNA and transcriptional response in grapefruit to the co-infection of CTV and Citrus dwarfing viroid.ResultsThe co-infection resulted in a difference in the expression of a number of sRNA species when comparing healthy and infected plants; the majority of these were derived from transcripts processed in a phased manner. Several RNA transcripts were also differentially expressed, including transcripts derived from two genes, predicted to be under the regulation of sRNAs. These genes are involved in plant hormone systems; one in the abscisic acid, and the other in the cytokinin regulatory pathway. Additional analysis of virus- and viroid-derived small-interfering RNAs (siRNAs) showed areas on the pathogen genomes associated with increased siRNA synthesis. Most interestingly, the starting position of the p23 silencing suppressor’s sub-genomic RNA generated a siRNA hotspot on the CTV genome.ConclusionsThis study showed the involvement of various genes, as well as endogenous and exogenous RNA-derived sRNA species in the plant-defence response. The results highlighted the role of sRNA-directed plant hormone regulation during biotic stress, as well as a counter-response of plants to virus suppressors of RNA-silencing.Electronic supplementary materialThe online version of this article (10.1186/s12985-017-0871-9) contains supplementary material, which is available to authorized users.

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Differential expression of miRNAs and associated gene targets in grapevine leafroll-associated virus 3-infected plants

Cited by 19 publications

References 49 publications

miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection

miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection

Comparative Analysis of MicroRNA Expression in Three Paulownia Species with Phytoplasma Infection

In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection

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