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

Chitarra, Walter; Pagliarani, Chiara; Abbà, Simona; Birello, Giancarlo; Rossi, Marika; Palmano, Sabrina; Marzachı̀, Cristina; Perrone, Irene; Gambino, Giorgio

doi:10.3389/fpls.2018.01034

Cited by 28 publications

(37 citation statements)

References 88 publications

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“…5c), in accordance with the expression profile of the ABA biosynthetic gene VvNCED2 (Fig. 5b) and sharing the same accumulation trend of JA previously reported for the same samples 35 .…”

Section: Fd-or Rec-induced Accumulation Of Abscisic Acid and Secondarsupporting

confidence: 90%

“…As transcript modulation can be influenced by several factors, including post-transcriptional regulation by microRNAs (miRNAs), transcriptomic data were put in correlation with outcomes from a previously published small RNA analysis 35 conducted on the same plant material. Among the 497 target genes of the miRNAs already validated in grapevine (miRVIT database, http:// mirvit.ipsp.cnr.it/), 163 transcripts underwent significant expression differences in at least one of the three comparisons (FD vs H, REC vs H and FD vs REC), and overall showed divergent expression profiles than those of related miRNAs ( Supplementary Table S4).…”

Section: Resultsmentioning

confidence: 99%

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Molecular memory of Flavescence dorée phytoplasma in recovering grapevines

et al. 2020

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Flavescence dorée (FD) is a destructive phytoplasma disease of European grapevines. Spontaneous and cultivardependent recovery (REC) may occur in the field in FD-infected vines starting the year following the first symptoms. However, the biological underpinnings of this process are still largely unexplored. In this study, transcriptome sequencing (RNAseq), whole-genome bisulphite sequencing (WGBS) and metabolite analysis were combined to dissect molecular and metabolic changes associated to FD and REC in leaf veins collected in the field from healthy (H), FD and REC plants of the highly susceptible Vitis vinifera 'Barbera'. Genes involved in flavonoid biosynthesis, carbohydrate metabolism and stress responses were overexpressed in FD conditions, whereas transcripts linked to hormone and stilbene metabolisms were upregulated in REC vines. Accumulation patterns of abscisic acid and stilbenoid compounds analysed in the same samples confirmed the RNAseq data. In recovery conditions, we also observed the persistence of some FD-induced expression changes concerning inhibition of photosynthetic processes and stress responses. Several differentially expressed genes tied to those pathways also underwent post-transcriptional regulation by microRNAs, as outlined by merging our transcriptomic data set with a previously conducted smallRNAseq analysis. Investigations by WGBS analysis also revealed different DNA methylation marks between REC and H leaves, occurring within the promoters of genes tied to photosynthesis and secondary metabolism. The results allowed us to advance the existence of a "molecular memory" of FDp infection, involving alterations in the DNA methylation status of REC plants potentially related to transcriptional reprogramming events, in turn triggering changes in hormonal and secondary metabolite profiles.

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“…5c), in accordance with the expression profile of the ABA biosynthetic gene VvNCED2 (Fig. 5b) and sharing the same accumulation trend of JA previously reported for the same samples 35 .…”

Section: Fd-or Rec-induced Accumulation Of Abscisic Acid and Secondarsupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Molecular memory of Flavescence dorée phytoplasma in recovering grapevines

et al. 2020

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“…Supplementary Materials: Supplementary Materials can be found at http://www.mdpi.com/1422-0067/21/18/ 6776/s1. References [73][74][75] are cited in the Supplementary Materials.…”

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confidence: 99%

The Molecular Priming of Defense Responses is Differently Regulated in Grapevine Genotypes Following Elicitor Application against Powdery Mildew

Pagliarani

Moine

Chitarra

et al. 2020

IJMS

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Molecular changes associated with response to powdery mildew (PM) caused by Erysiphe necator have been largely explored in Vitis vinifera cultivars, but little is known on transcriptional and metabolic modifications following application of resistance elicitors against this disease. In this study, the whole transcriptome sequencing, and hormone and metabolite analyses were combined to dissect long-term defense mechanisms induced by molecular reprogramming events in PM-infected ‘Moscato’ and ‘Nebbiolo’ leaves treated with three resistance inducers: acibenzolar-S-methyl, potassium phosphonate, and laminarin. Although all compounds were effective in counteracting the disease, acibenzolar-S-methyl caused the most intense transcriptional modifications in both cultivars. These involved a strong down-regulation of photosynthesis and energy metabolism and changes in carbohydrate accumulation and partitioning that most likely shifted the plant growth-defense trade-off towards the establishment of disease resistance processes. It was also shown that genotype-associated metabolic signals significantly affected the cultivar defense machinery. Indeed, ‘Nebbiolo’ and ‘Moscato’ built up different defense strategies, often enhanced by the application of a specific elicitor, which resulted in either reinforcement of early defense mechanisms (e.g., epicuticular wax deposition and overexpression of pathogenesis-related genes in ‘Nebbiolo’), or accumulation of endogenous hormones and antimicrobial compounds (e.g., high content of abscisic acid, jasmonic acid, and viniferin in ‘Moscato’).

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“…Moreover, the predicted novel miRNAs were searched in miRVIT [27] database to annotate novel miRNAs had reported in grapevine before. In addition, the novel miRNA also aligned with mature miRNAs database in the miRBase 21 by default Parameter (Evalue cutoff ≤ 10, Mismatch penalty = -4, Match score ≥ 60).…”

Section: Identification Of Known and Novel Vvi-mirnasmentioning

confidence: 99%

“…Moreover, a microRNA expression atlas of grapevine was analyzed including 70 small RNA libraries containing many tissues [25,26]. In addition, Chitarra et al integrated a novel miRNA database "miRVIT" inferred from published small RNA libraries which was not uploaded in miRBase database [27]. However, the miRNA derived from grapevine root system wasless in the statistical sequencing data.…”

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confidence: 99%

Transcriptome analysis of miRNAs expression reveals novel insights into root formation under Root restriction cultivation in grapevine (Vitis vinifera L.)

Gao

Zahid

et al. 2020

Preprint

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Background: Root restriction cultivation not only promotes maturation and quality of fruit, but optimizes the architecture of root, especially in enhancing the occurrence of adventitious and lateral roots. While the molecular mechanism of this phenotype is still unknown. Results: In this study, the development of roots was observed at 12 different time points under Root restriction and normal cultivations (control). Root phenotype showed a significantly different feature start from the seventh sampling, mainly in the increasing of adventitious roots numbers, degeneration of root tip and subsequent mass of lateral roots development. The 7th and 12th sampling of two different cultivations, named nR7, nR12, RR7, and RR12, were selected for small RNA sequencing. 214,439,588 raw reads were obtained and 168,741,687 clean reads were remained after the quality control steps, and finally got a total of 153 known miRNAs, and 119 predicted novel miRNAs. The predicted novel miRNAs blasted with the miRVIT and miRBase databases simultaneously. 96 new family members of grapevine miRNA and 23 grapevine-specific novel miRNAs were obtained. Differentially expressed miRNAs (DEMs) analysis showed that 26 and 33 miRNAs were differentially expressed in two different cultivation models (RR7 vs nR7; RR12 vs nR12), while 26 and 32 DEMs were obtained in different root development stages (nR12 vs nR7; RR12 vs RR7). MiRNA expression levels analysis found that conserved miRNA s were in higher expression level than novel miRNAs. The predicted target genes of DEMs were annotated on a variety of biological processes, and 24 participated in root development. An analysis of vvi-miR160 family members revealed that vvi-miR160c was highly expressed in grapevine root, indicating the potential role of miR160c in root development, which in accordance with the previous report in Arabidopsis . Conclusions: Multiple miRNAs were jointly to regulate root development on Root restriction condition, mainly in lateral root development. And the specific expression of vvi-miR160c in the apex may be the main cause of apical degradation. Moreover, there were multiple miRNAs related to biotic or abiotic stresses, which indicated that multiple minor stresses exist in root development after Root restriction cultivation.

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

Cited by 28 publications

References 88 publications

Molecular memory of Flavescence dorée phytoplasma in recovering grapevines

Molecular memory of Flavescence dorée phytoplasma in recovering grapevines

The Molecular Priming of Defense Responses is Differently Regulated in Grapevine Genotypes Following Elicitor Application against Powdery Mildew

Transcriptome analysis of miRNAs expression reveals novel insights into root formation under Root restriction cultivation in grapevine (Vitis vinifera L.)

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