De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina

Ahn, Soon Young; Kim, Seon Ae; Jo, Sung Hwan; Yun, Hae Keun

doi:10.1017/s1479262114000410

Cited by 16 publications

(22 citation statements)

References 11 publications

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“…The expression of Vf GST26625 was up-regulated, while that of the other genes was down-regulated in all grapevine leaves inoculated with each pathogen. The expression kinetics from the real-time PCR results were similar to those of previous transcripts analyses (Ahn et al 2014) In leaves inoculated with B. cinerea, expression of the Vf GST13892, Vf GST29294, Vf GST3450, and Vf GST774 genes was down-regulated relative to the control, while Vf GST26625 exhibited delayed and sustained up-regulation of transcription (Fig. 3A).…”

Section: Fig 2 Phylogenetic Analysis Of Glutathione S-transferases supporting

confidence: 83%

“…Five of the 17 GST transcripts showing more than 500 read counts identified upon transcriptome analysis of V. flexuosa inoculated with E. ampelina (Ahn et al 2014) were selected for characterization of their structures and evaluation of their differential expression against pathogen attacks. In this study, these genes were designated Vf GST26625 (V. flexuosa GST, Locus 26625), Vf GST13892 The deduced amino acid sequences of GST genes in V. vinifera and V. flexuosa transcripts are shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…All reactions were performed in triplicate to ensure consistency of the results. Five of the GST differentially expressed genes identified upon transcriptome analysis of V. flexuosa inoculated with E. ampelina were selected (Ahn et al 2014), and specific primers for real-time PCR were designed by alignment of their nucleotide sequences (Table 1). In order to validate the pathogen infection, the pathogenesis-related 1 (PR1)…”

Section: Real-time Pcrmentioning

confidence: 99%

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Glutathione S-Transferase Genes Differently Expressed by pathogen-Infection in Vitis flexuosa

Ahn¹,

Kim²,

Yun³

2016

Plant Breed. Biotech

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2016 (February) ABSTRACT Glutathione S-transferase (GST) genes from transcripts of Vitis flexuosa leaves infected with Elsinoe ampelina were characterized and analyzed for their expression using primers based on specific regions. Comparison of deduced amino acid sequences from GST transcripts of V. flexuosa showed that the score of the deduced amino acid identity ranged from 43.38% (Vf GST26625 and Vf GST774) to 6.67% (Vf GST13892 and Vf GST774). Primary and secondary structure analysis was performed using the ProtParam and Self-Optimized Prediction Method with Alignment software. A phylogenetic tree was constructed from the GST proteins by the neighbor joining method using MEGA 6.0 to investigate the relationship among Vf GST, VvGST, and At GST proteins. To evaluate the differential expression pattern of GST genes by real-time polymerase chain reaction (PCR), primers specific to unique regions in each gene were obtained by alignment of the sequences. Real-time PCR revealed that GST genes were expressed differentially in the leaves of V. flexuosa infected with Botrytis cinerea, E. ampelina, and Rhizobium vitis. The expression of Vf GST26625 was up-regulated, while that of others were down-regulated among five GSTs in all grapevine leaves inoculated with each pathogen. The results provided herein improve our understanding of defense responses to various pathogen attacks in grapevines.

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Section: Fig 2 Phylogenetic Analysis Of Glutathione S-transferases supporting

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Real-time Pcrmentioning

confidence: 99%

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Glutathione S-Transferase Genes Differently Expressed by pathogen-Infection in Vitis flexuosa

Ahn¹,

Kim²,

Yun³

2016

Plant Breed. Biotech

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“…Although cultivated grapevines (V. vinifera L.) are highly susceptible to several diseases, some wild cultivars such as V. riparia, V. rupestris, V. rotundifolia and V. flexuosa are reportedly resistant to several important grapevine diseases (Eibach et al 1989;Kortekamp et al 2008;Ahn et al 2012). In a previous study, we found several transcripts of EDS1-like genes with differential expression levels in the transcriptome of V. flexuosa infected with E. ampelina (Ahn et al 2014). Therefore, in this study, we cloned three EDS1-like genes in V. flexuosa to characterize these genes by analyzing their structural features and phylogenetic relationship with other plants, and by investigating their expression patterns in response to infection by E. ampelina and R. vitis.…”

Section: Introductionmentioning

confidence: 93%

Three transcripts of EDS1-like genes respond differently to Vitis flexuosa infection

Islam

Yun

2017

J Plant Biotechnol

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract Enhanced disease susceptibility1 (EDS1) is a regulator of basal defense responses required for resistance mediated by TIR-NBS-LRR containing R proteins. We identified three transcripts of EDS1-like genes encompassing diverse/ separate expression patterns, based on the transcriptome analysis by Next Generation Sequencing (NGS) of V. flexuosa inoculated with Elsinoe ampelina. These genes were designated VfEDL1 (Vitis flexuosa Enhanced Disease Susceptibility1-like1), VfEDL2 and VfEDL3, and contained 2464, 1719 and 1599 bp, with 1791, 1227 and 1599 bp open reading frames (ORFs), encoding proteins of 596, 408 and 532 amino acids, respectively. The predicted amino acid sequences of all three genes showed the L-family lipase-like domain (class 3 lipase domain), and exhibited a potential lipase catalytic triad, aspartic acid, histidine and serine in the conserved G-X-S-X-G. All three VfEDL genes were upregulated at 1 hpi against the bacterial and fungal pathogens Rizhobium vitis and E. ampelina, respectively, except VfEDL1, which was downregulated against E. ampelina at all time points. Against E. ampelina, VfEDL2 and VfEDL3 showed downregulated expression at later time points. When evaluated against R. vitis, VfEDL1 showed downregulated expression at all time points after 1 hpi, while VfEDL3 showed upregulation up to 24 hpi. Based on the expression response, all three genes may be involved in plant resistant responses against R. vitis, and VfEDL2 and VfEDL3 show additional resistant responses against E. ampelina infection.

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“…All reactions were performed in triplicate. Among 28 DEGs identified upon transcriptome analysis of V. flexuosa inoculated with E. ampelina (Ahn et al 2014), six loci showing variation with more than 100 transcripts were selected for evaluation of their differential expression against pathogen attacks. Four of these β-1,3-glucanase genes showed differential expression in response to E. ampelina inoculation of grapevines, therefore, specific primers for real-time PCR were designed by alignment of the nucleotide sequences obtained from the V. flexuosa transcriptome data.…”

Section: Real-time Pcr Analysismentioning

confidence: 99%

Differential Expression of β-1,3-Glucanase Transcripts Induced by Pathogens in the Leaves of Vitis flexuosa

Ahn

Kim

Yun

2014

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The differential expression of β-1,3-glucanase genes in the leaves of Vitis flexuosa induced by fungal and bacterial pathogen infections was investigated. The nucleotide and deduced amino acid sequences of β-1,3-glucanase genes from the transcripts of V. flexuosa were compared. The percentage similarity of deduced amino acid ranged from 22.0% between VfGlu34359 and VfGlu48103 to 96.9% in VvGlu2735 and VvGlu48103. To demonstrate the differential expression pattern of β-1,3-glucanase genes, primers specific to unique regions in each gene were obtained by alignment of the sequences. Accumulation patterns of β-1,3-glucanase mRNAs in the leaves of V. flexuosa were induced differentially and were dependent on the pathogens used including Botrytis cinerea, Colletotrichum acutatum, Elsinoe ampelina, and Rhizobium vitis. This study provides useful information that will improve our understanding of grapevine defense responses to various pathogen attacks.

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De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina

Cited by 16 publications

References 11 publications

Glutathione S-Transferase Genes Differently Expressed by pathogen-Infection in Vitis flexuosa

Glutathione S-Transferase Genes Differently Expressed by pathogen-Infection in Vitis flexuosa

Three transcripts of EDS1-like genes respond differently to Vitis flexuosa infection

Differential Expression of β-1,3-Glucanase Transcripts Induced by Pathogens in the Leaves of Vitis flexuosa

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