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Background: Ultraviolet (UV) radiation modulates secondary metabolism in the skin of Vitis vinifera L. berries, which affects the final composition of both grapes and wines. The expression of several phenylpropanoid biosynthesis-related genes is regulated by UV radiation in grape berries. However, the complete portion of transcriptome and ripening processes influenced by solar UV radiation in grapes remains unknown.Results: Whole genome arrays were used to identify the berry skin transcriptome modulated by the UV radiation received naturally in a mid-altitude Tempranillo vineyard. UV radiation-blocking and transmitting filters were used to generate the experimental conditions. The expression of 121 genes was significantly altered by solar UV radiation. Functional enrichment analysis of altered transcripts mainly pointed out that secondary metabolism-related transcripts were induced by UV radiation including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes and monoterpenoid biosynthetic genes. Berry skin phenolic composition was also analysed to search for correlation with gene expression changes and UV-increased flavonols accumulation was the most evident impact. Among regulatory genes, novel UV radiation-responsive transcription factors including VvMYB24 and three bHLH, together with known grapevine UV-responsive genes such as VvMYBF1, were identified. A transcriptomic meta-analysis revealed that genes up-regulated by UV radiation in the berry skin were also enriched in homologs of Arabidopsis UVR8 UV-B photoreceptor-dependent UV-B -responsive genes. Indeed, a search of the grapevine reference genomic sequence identified UV-B signalling pathway homologs and among them, VvHY5-1, VvHY5-2 and VvRUP were up-regulated by UV radiation in the berry skin.Conclusions: Results suggest that the UV-B radiation-specific signalling pathway is activated in the skin of grapes grown at mid-altitudes. The biosynthesis and accumulation of secondary metabolites, which are appreciated in winemaking and potentially confer cross-tolerance, were almost specifically triggered. This draws attention to viticultural practices that increase solar UV radiation on vineyards as they may improve grape features. © 2014 Carbonell-Bejerano et al.; licensee BioMed Central Ltd. ; ENO and JMA are grateful to the Ministerio de Economía y Competitividad of Spain and the Fondo Europeo de Desarrollo Regional (FEDER) for financial support (Project CGL2011-26937). This study was funded in part by Project BIO2011-026229 from the Spanish MINECO. Microarray hybridizations were carried out at the Genomics Unit of the National Centre for Biotechnology, CNB-CSIC, Madrid, Spain. The present work is integrated in the COST (European Cooperation in Science and Technology) Action FA0906 of the European Union "UV-B radiation: a specific regulator of plant growth and food quality in a changing climate" as well as COST Action FA1106 "Quality fruit". ; Peer Reviewed

Díaz-Riquelme, José et al. ; [Background] The two-spotted spider mite, Tetranychus urticae, is an extreme generalist plant pest. Even though mites can feed on many plant species, local mite populations form host races that do not perform equally well on all potential hosts. An acquisition of the ability to evade plant defenses is fundamental for mite's ability to use a particular plant as a host. Thus, understanding the interactions between the plant and mites with different host adaptation status allows the identification of functional plant defenses and ways mites can evolve to avoid them. ; [Results] The grapevine genome-wide transcriptional responses to spider mite strains that are non-adapted and adapted to grapevine as a host were examined. Comparative transcriptome analysis of grapevine responses to these mite strains identified the existence of weak responses induced by the feeding of the non-adapted strain. In contrast, strong but ineffective induced defenses were triggered upon feeding of the adapted strain. A comparative meta-analysis of Arabidopsis, tomato and grapevine responses to mite feeding identified a core of 36 highly conserved genes involved in the perception, regulation and metabolism that were commonly induced in all three species by mite herbivory. ; [Conclusions] This study describes the genome-wide grapevine transcriptional responses to herbivory of mite strains that differ in their ability to use grapevine as a host. It raises hypotheses whose testing will lead to our understanding of grapevine defenses and mite adaptations to them. ; This Project was funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-046, to MG and VG) and Ontario Research Fund–Global Leadership in Genomics and Life Sciences (GL2-01-035, to MG and VG), the Spanish Ministry of Science and Innovation (AGL2011-24584, to IPM), the Spanish MINECO grant BIO2011-026229 to JMZ. JG was a recipient of a Contract Ramon y Cajal from Spanish MINECO (RYC-2011-07791). SB was partially supported by the Fund for Scientific Research Flanders, grant G.0093.12 N to TVL. ; Peer Reviewed

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae. ; This material is based upon work that is supported by the Minnesota Department of Agriculture (J.A., K.F., R.C.) and by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award numbers 2018-67009-27374 (J.A., R.C., K.F.), and 2019-67009-29004 (M.D.M, J.S.) and the Agriculture and Food Research Initiative Competitive Grant No. 2019-69012-29851 (M.D.M, R.C., J.S.). This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomics Science Program grant no. DE-SC0021286 (M.D.M, R.C.). This work was further funded by the Austrian Academy of Sciences (C.B., I.R.A., K.J., D.R.C.); the Max Planck Society (D.W., A.C.G., P.C.B., C.L.); the European Union's Horizon 2020 research and innovation programme by the European ...