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

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 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

The transcription factor VviNAC60 regulates senescence- and ripening-related processes in grapevine

: Grapevine (Vitis vinifera L.) is one of the most widely cultivated fruit crops because the winemaking industry has huge economic relevance worldwide. Uncovering the molecular mechanisms controlling the developmental progression of plant organs will prove essential for maintaining high-quality grapes, expressly in the context of climate change, which impairs the ripening process. Through a deep inspection of transcriptomic data, we identified VviNAC60, a member of the NAC transcription factor family, as a putative regulator of grapevine organ maturation. We explored VviNAC60 binding landscapes through DNA affinity purification followed by sequencing and compared bound genes with transcriptomics datasets from grapevine plants stably and transiently overexpressing VviNAC60 to define a set of high-confidence targets. Among these, we identified key molecular markers associated with organ senescence and fruit ripening. Physiological, metabolic, and promoter activation analyses showed that VviNAC60 induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of STAY-GREEN PROTEIN 1 (VviSGR1) and VviMYBA1, respectively, with the latter being up-regulated through a VviNAC60-VviNAC03 regulatory complex. Despite sharing a closer phylogenetic relationship with senescence-related homologues to the NAC transcription factor AtNAP, VviNAC60 complemented the non-ripening(nor) mutant phenotype in tomato (Solanum lycopersicum), suggesting a dual role as an orchestrator of both ripening- and senescence-related processes. Our data support VviNAC60 as a regulator of processes initiated in the grapevine vegetative- to mature-phase organ transition and therefore as a potential target for enhancing the environmental resilience of grapevine by fine-tuning the duration of the vegetative phase

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development.

BACKGROUND: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. RESULTS: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. CONCLUSIONS: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility

Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. ‘Gamay’ grapevines (Vitis vinifera L.)

In most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while ‘teinturier’ cultivars also accumulate anthocyanins in the pulp. Here, we investigated the teinturier cvs. ‘Gamay de Bouze’ and ‘Gamay Fréaux’ (two somatic variants of the white-fleshed cv. ‘Gamay’) through metabolic and transcript analysis to clarify whether these two somatic variants have the same anthocyanin accumulation pattern in the skin and pulp, and whether primary metabolites are also affected. The skin of the three cultivars and the pulp of ‘Gamay de Bouze’ begun to accumulate anthocyanins at the onset of berry ripening. However, the pulp of ‘Gamay Fréaux’ exhibited a distinct anthocyanin accumulation pattern, starting as early as fruit set with very low level of sugars. The highest level of anthocyanins was found in ‘Gamay Fréaux’ skin, followed by ‘Gamay de Bouze’ and ‘Gamay’. Consistently, the transcript abundance of genes involved in anthocyanin biosynthesis were in line with the anthocyanin levels in the three cultivars. Despite no evident differences in pulp sugar content, the concentration of glucose and fructose in the skin of ‘Gamay Fréaux’ was only half of those in the skin of ‘Gamay’ and ‘Gamay de Bouze’ throughout all berry ripening, suggesting an uncoupled accumulation of sugars and anthocyanins in ‘Gamay Fréaux’. The study provides a comprehensive view of metabolic consequences in grape somatic variants and the three almost isogenic genotypes can serve as ideal reagents to further uncover the mechanisms underlying the linkage between sugar and anthocyanin accumulation.This research was supported partly by the National Key R&D Program of China (2018YFD1000200) and was conducted as part of the LIA INNOGRAPE International Associated Laboratory.Peer reviewe