Transcriptomic and metabolomic networks in the grape berry illustrate that it takes more than flavonoids to fight against ultraviolet radiation

Plants are constantly challenged by environmental fluctuations. In response, they have developed a wide range of morphological and biochemical adaptations committed to ameliorate the effects of abiotic stress. When exposed to higher solar radiation levels, plants activate the synthesis of a large set of enzymes and secondary metabolites as part of a complex sunscreen and antioxidant defense mechanism. Grapevine (Vitis vinifera L.) has become a widely used system for studying adaptive responses to this type of stress since changes in berry composition, positively influenced by increased ultraviolet (UV) radiation levels, improve the quality of wines subsequently produced. Despite the fact that most of the attention has been directed toward the synthesis of flavonoids, recent transcriptomic and metabolomic studies have shown that stilbenoids and isoprenoids (e.g., terpenes and carotenoids) are also an important part of the grape UV-response machinery. This minireview focuses on the latest findings referring to the metabolic responses of grapes to UV radiation and proposes a model for its transcriptional control. Depending on the berry developmental stage and the type of radiation (i.e., irradiance level, exposure length), increased UV levels activate different metabolic pathways through the activity of master regulators belonging to the basic Leucine Zipper Domain (bZIP) and R2R3-MYB transcription factor families. This transcriptional control is influenced by the interaction of other environmental factors such as light, temperature or soil water availability. In grapevine, phenylpropanoids are part of, but are not the whole story, in the fight against radiation damage

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

<p>Abstract</p> <p>Background</p> <p>The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality.</p> <p>Results</p> <p>We describe and classify 108 members of the grape <it>R2R3 MYB </it>gene subfamily in terms of their genomic gene structures and similarity to their putative <it>Arabidopsis thaliana </it>orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across <it>Arabidopsis </it>and <it>Vitis</it>, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the <it>Arabidopsis </it>and rice MYB subfamilies. Two anthocyanin <it>MYBA </it>related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11.</p> <p>Conclusion</p> <p>This genome wide transcription factor analysis in <it>Vitis </it>suggests that clade-specific grape <it>R2R3 MYB </it>genes are expanded while other MYB genes could be well conserved compared to <it>Arabidopsis</it>. <it>MYB </it>gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.</p

Beyond COST Action INTEGRAPE: The Grapevine Genomics Encyclopedia Initiative

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A COMPASS for VESPUCCI: a FAIR way to explore the grapevine transcriptomic landscape

7openInternational coauthor/editoropenMoretto, M.; Sonego, P.; Pilati, S.; Matus, J.T.; Costantini, L.; Malacarne, G.; Engelen, K.Moretto, M.; Sonego, P.; Pilati, S.; Matus, J.T.; Costantini, L.; Malacarne, G.; Engelen, K

Genetic and histological studies on the delayed systemic movement of Tobacco Mosaic Virus in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Viral infections and their spread throughout a plant require numerous interactions between the host and the virus. While new functions of viral proteins involved in these processes have been revealed, current knowledge of host factors involved in the spread of a viral infection is still insufficient. In <it>Arabidopsis thaliana</it>, different ecotypes present varying susceptibilities to <it>Tobacco mosaic virus </it>strain U1 (TMV-U1). The rate of TMV-U1 systemic movement is delayed in ecotype Col-0 when compared with other 13 ecotypes.</p> <p>We followed viral movement through vascular tissue in Col-0 plants by electronic microscopy studies. In addition, the delay in systemic movement of TMV-U1 was genetically studied.</p> <p>Results</p> <p>TMV-U1 reaches apical leaves only after 18 days post rosette inoculation (dpi) in Col-0, whereas it is detected at 9 dpi in the Uk-4 ecotype. Genetic crosses between Col-0 and Uk-4 ecotypes, followed by analysis of viral movement in F₁and F₂populations, revealed that this delayed movement correlates with a recessive, monogenic and nuclear locus. The use of selected polymorphic markers showed that this locus, denoted <it>DSTM1 </it>(Delayed Systemic Tobamovirus Movement 1), is positioned on the large arm of chromosome II. Electron microscopy studies following the virion's route in stems of Col-0 infected plants showed the presence of curved structures, instead of the typical rigid rods of TMV-U1. This was not observed in the case of TMV-U1 infection in Uk-4, where the observed virions have the typical rigid rod morphology.</p> <p>Conclusion</p> <p>The presence of defectively assembled virions observed by electron microscopy in vascular tissue of Col-0 infected plants correlates with a recessive delayed systemic movement trait of TMV-U1 in this ecotype.</p

Vitis OneGenE: a causality-based approach to generate gene networks in Vitis vinifera sheds light on the laccase and dirigent gene families

9openInternationalBothThe abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.openPilati, Stefania; Malacarne, Giulia; Navarro-Payá, David; Tomè, Gabriele; Riscica, Laura; Cavecchia, Valter; Matus, José Tomás; Moser, Claudio; Blanzieri, EnricoPilati, S.; Malacarne, G.; Navarro-Payá, D.; Tomè, G.; Riscica, L.; Cavecchia, V.; Matus, J.T.; Moser, C.; Blanzieri, E

The grapevine guard cell-related VvMYB60 transcription factor is involved in the regulation of stomatal activity and is differentially expressed in response to ABA and osmotic stress

- Background: Under drought, plants accumulate the signaling hormone abscisic acid (ABA), which induces the rapid closure of stomatal pores to prevent water loss. This event is trigged by a series of signals produced inside guard cells which finally reduce their turgor. Many of these events are tightly regulated at the transcriptional level, including the control exerted by MYB proteins. In a previous study, while identifying the grapevine R2R3 MYB family, two closely related genes, VvMYB30 and VvMYB60 were found with high similarity to AtMYB60, an Arabidopsis guard cell-related drought responsive gene. - Results: Promoter-GUS transcriptional fusion assays showed that expression of VvMYB60 was restricted to stomatal guard cells and was attenuated in response to ABA. Unlike VvMYB30, VvMYB60 was able to complement the loss-of-function atmyb60-1 mutant, indicating that VvMYB60 is the only true ortholog of AtMYB60 in the grape genome. In addition, VvMYB60 was differentially regulated during development of grape organs and in response to ABA and drought-related stress conditions. - Conclusions: These results show that VvMYB60 modulates physiological responses in guard cells, leading to the possibility of engineering stomatal conductance in grapevine, reducing water loss and helping this species to tolerate drought under extreme climatic conditions

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)

[EN] Soil flooding is a compound abiotic stress that alters soil properties and limits atmospheric gas diffusion (O-2 and CO2) to the roots. The involvement of abscisic acid (ABA) in the regulation of soil flooding-specific genetic and metabolic responses has been scarcely studied despite its key importance as regulator in other abiotic stress conditions. To attain this objective, wild type and ABA-deficient tomatoes were subjected to short-term (24 h) soil waterlogging. After this period, gas exchange parameters were reduced in the wild type but not in ABA-deficient plants that always had higher E and g(s). Transcript and metabolite alterations were more intense in waterlogged tissues, with genotype-specific variations. Waterlogging reduced the ABA levels in the roots while inducing PYR/PYL/RCAR ABA receptors and ABA-dependent transcription factor transcripts, of which induction was less pronounced in the ABA-deficient genotype. Ethylene/O-2-dependent genetic responses (ERFVIIs, plant anoxia survival responses, and genes involved in the N-degron pathway) were induced in hypoxic tissues independently of the genotype. Interestingly, genes encoding a nitrate reductase and a phytoglobin involved in NO biosynthesis and scavenging and ERFVII stability were induced in waterlogged tissues, but to a lower extent in ABA-deficient tomato. At the metabolic level, flooding-induced accumulation of Ala was enhanced in ABA-deficient lines following a differential accumulation of Glu and Asp in both hypoxic and aerated tissues, supporting their involvement as sources of oxalacetate to feed the tricarboxylic acid cycle in waterlogged tissues and constituting a potential advantage upon long periods of soil waterlogging. The promoter analysis of upregulated genes indicated that the production of oxalacetate from Asp via Asp oxidase, energy processes such as acetyl-CoA, ATP, and starch biosynthesis, and the lignification process were likely subjected to ABA regulation. Taken together, these data indicate that ABA depletion in waterlogged tissues acts as a positive signal, inducing several specific genetic and metabolic responses to soil flooding.This work was supported by the Spanish Ministerio de Economia y Competitividad, Universitat Jaume I and Generalitat Valenciana/Fondo Europeo de Desarrollo Regional (FEDER), co-funded through grant nos. AGL2016-76574-R, UJI-B201623, UJI-B2016-24, IDIFEDER/2018/010, and UJI-B2019-24 to AG-C, VA, and MG-G, respectively. CD was supported by UJI PICD program. MG-G and JM were supported by Ramon y Cajal contracts from Spanish Ministerio de Economia y Competitividad (RYC-2016-19325 and RYC-201723645, respectively). JR was supported by a Juan de la CiervaFormacion contract from the Spanish Ministerio de Economia y Competitividad (FJCI-2016-28601).De Ollas, C.; González-Guzmán, M.; Pitarch, Z.; Matus, JT.; Candela, H.; Rambla Nebot, JL.; Granell Richart, A.... (2021). Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill). Frontiers in Plant Science. 12:1-20. https://doi.org/10.3389/fpls.2021.613059S1201

The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications

Inspection of the grapevine BURP superfamily highlights an expansion of RD22 genes with distinctive expression features in berry development and ABA-mediated stress responses

The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of polygalacturonases. In grapevine, a RD22 gene has been identified but putative paralogs are also found in the grape genome, possibly forming a large RD22 family in this species. In this work, we searched for annotations containing BURP domains in the Vitis vinifera genome. Nineteen proteins were defined by a comparative analysis between the two genome predictions and RNA-Seq data. These sequences were compared to other plant BURPs identified in previous genome surveys allowing us to reconceive group classifications based on phylogenetic relationships and protein motif occurrence. We observed a lineage-specific evolution of the RD22 family, with the biggest expansion in grapevine and poplar. In contrast, rice, sorghum and maize presented highly expanded monocot-specific groups. The Vitis RD22 group may have expanded from segmental duplications as most of its members are confined to a region in chromosome 4. The inspection of transcriptomic data revealed variable expression of BURP genes in vegetative and reproductive organs. Many genes were induced in specific tissues or by abiotic and biotic stresses. Three RD22 genes were further studied showing that they responded oppositely to ABA and to stress conditions. Our results show that the inclusion of RNA-Seq data is essential while describing gene families and improving gene annotations. Robust phylogenetic analyses including all BURP members from other sequenced species helped us redefine previous relationships that were erroneously established. This work provides additional evidence for RD22 genes serving as marker genes for different organs or stresses in grapevine