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264 results for “grapevine”
Data from: Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development
We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.
Data from: Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines
The wild grapevine, Vitis vinifera L. ssp sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain natural populations of Vitis vinifera ssp sylvestris can still be found along river banks. In this work we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analyzed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software STRUCTURE we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships among wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current western cultivars.
Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew
Adaptation produces hard or soft selective sweeps depending on the supply of adaptive genetic polymorphism. The evolution of pesticide resistance in parasites is a striking example of rapid adaptation that can shed light on selection processes. Plasmopara viticola, which causes grapevine downy mildew, forms large populations, in which resistance has rapidly evolved due to excessive fungicide use. We investigated the pathways by which fungicide resistance has evolved in this plant pathogen, to determine whether hard or soft selective sweeps were involved. An analysis of nucleotide polymorphism in 108 field isolates from the Bordeaux region revealed recurrent mutations of cytb and CesA3 conferring resistance to quinone outside inhibiting (QoI) and carboxylic acid amide (CAA) fungicides, respectively. Higher levels of genetic differentiation were observed for nucleotide positions involved in resistance than for neutral microsatellites, consistent with local adaptation of the pathogen to fungicide treatments. No hitchhiking was found between selected sites and neighbouring polymorphisms in cytb and CesA3, confirming multiple origins of resistance alleles. We assessed resistance costs, by evaluating the fitness of the 108 isolates through measurements of multiple quantitative pathogenicity traits under controlled conditions. No significant differences were found between sensitive and resistant isolates, suggesting that fitness costs may be absent or negligible. Our results indicate that the rapid evolution of fungicide resistance in P. viticola has involved a soft sweep.
Data from: Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew
An understanding of the evolution of pathogen quantitative traits in response to host selective pressures is essential for the development of durable management strategies for resistant crops. However, we still lack experimental data on the effects of partial host resistance on multiple phenotypic traits (aggressiveness) and evolutionary strategies in pathogens. We performed a cross-inoculation experiment with four grapevine hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola) sampled from susceptible and partially resistant grapevine varieties. We analysed the neutral and adaptive genetic differentiation of five quantitative traits relating to pathogen transmission. Isolates from resistant hosts were more aggressive than isolates from susceptible hosts, as they had a shorter latency period and higher levels of spore production. This pattern of adaptation contrasted with the lack of neutral genetic differentiation, providing evidence for directional selection. No specificity for a particular host variety was detected. Adapted isolates had traits that were advantageous on all resistant varieties. There was no fitness cost associated with this genetic adaptation, but several trade-offs between pathogen traits were observed. These results should improve the accuracy of prediction of fitness trajectories for this biotrophic pathogen, an essential element for the modelling of durable deployment strategies for resistant varieties.
FIGURES 1–12 in A new Neotropical sharpshooter genus Spinagonalia (Insecta, Hemiptera, Cicadellidae, Cicadellinae) with description of a new species from Citrus orchards and grapevines
FIGURES 1–12. Spinagonalia rubrovittata gen. nov. and sp. nov. (Paratypes). 1–6, male. 1—Head, pronotum and scutellum, dorsal view; 2—pygofer, lateral view; 3—valve and subgenital plate, ventral view; 4—style, connective and paraphysis, dorsal view; 5—aedeagus and anal tube, lateral view; 6—apex of aedeagus, posterior view; 7–12, female. 12 —pygofer and sternite VII, lateral view; 8—sternite VII, ventral view; 9—sternite VIII, dorsal view; 10—base of the first valvula, lateral view; 11—first valvula apex, lateral view; 12—second valvula, lateral view.
FIGURE 1 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 1. Triophtydeus lebruni (Female) A. Dorsal view; B. Anogenital area; C. Palp; D. Leg I; E. Leg IV.
FIGURE 8 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 8. Pretydeus henriandrei (Female) A. Dorsal view; B. Seta c1 on dorsal idiosoma. C. Palp; D. Cheliceral stilettos; E. Leg I; F. Leg II.
FIGURE 6 in Tydeid and triophtydeid mites (Acari: Tydeoidea) associated with grapevine (Vitaceae: Vitis spp.) in Brazil, with the descriptions of species of Prelorryia (André, 1980) and Tydeus Koch, 1835
FIGURE 6. Tydeus manoi sp. nov. (Female) A. Dorsal view; B. Anogenital area; C. Palp; D. Leg I; E. Leg II; F. Leg III.
Replication data and analysis code for the article "Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France"
<p>This deposit contains the dataset used in the article "Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France" in the form of a RData file, directly loadable in R, as well as the Rmd script used to analyse the data and produce the figures.</p>
Integrative genomics reveals the polygenic basis of seedless in grapevine (Vitis vinifera L.)
<p>The publicly accessible genome data comprises:</p> <p>1) Haplotype genomes of 'Thompson Seedless' (TS) and 'Black Monukka' (BM) (.fa files) along with annotations (.gff files),</p> <p>2) Cytoplasmic genomes (mitochondria and chloroplasts),</p> <p>3) Annotations for tandem repeats,</p> <p>4) EDTA annotations (available at https://github.com/oushujun/EDTA),</p> <p>5) panTE (Transposable element) annotations (available at https://github.com/unavailable-2374/TE_Detective-Annotation).</p> <p>Additionally,</p> <p>6) Several genomes, such as 'Cabernet Sauvignon', 'Black Corinth Seedless', and 'Black Corinth Seeded', were restructured based on PN_T2T genome similarity using RagTag (https://github.com/malonge/RagTag).</p> <p>Among these resources,</p> <p>7) The 'Cabernet Sauvignon' genome was annotated using PN_T2T annotation through Liftoff (https://github.com/agshumate/Liftoff), and it maintains consistent gene IDs between the 'Cabernet Sauvignon' genome and PN_T2T.</p> <p>Furthermore, we have retained the original data for the protein files of 'Black Corinth Seedless' and 'Black Corinth Seeded'.<br> <br> If you have any questions, please let me know: 571720850@qq.com</p>
Dataset of Grapevine roots with length, diameter, and color annotations
<p>Data includes 531 annotated images of grapevines roots which were acquired from 40 tubes across a range of depths in the soil profile in the Ramat Negev region, Israel, in August 2012 to December 2013. There were five tubes for each combination of cultivar, irrigation treatment, and tube distance from the trunk. The tubes were 2 m long, with a 6 cm outer diameter and 5.15 cm inner diameter. Data was acquired with manual MR acquisition system using a BTC-2, Bartz Technology Co. (Carpinteria, California, USA) MR camera system with its default settings. The camera was attached to an indexing handle and controlled using a laptop-computer-based image capture system (I-CAP, Bartz Technology Co., Carpentaria, California, USA). The images were taken by an older type of manual MR system, where an image view an area 16.5 × 14 mm<sup>2</sup> at a resolution of 754 × 648 pixels.</p> <p> </p> <p>Additional 132 annotated images corresponding to two different treatment were added.</p> <p>Images were annotated using root-image analysis software Rootfly Version 2.0.2 (Clemson University, South Carolina, USA; <a href="http://www.ces.clemson.edu/~stb/rootfly/">http://www.ces.clemson.edu/~stb/rootfly/</a>).</p>
Supplementary material 1 from: van Nieukerken EJ, Geertsema H (2015) A new leafminer on grapevine and Rhoicissus (Vitaceae) in South Africa within an expanded generic concept of Holocacista (Insecta, Lepidoptera, Heliozelidae). ZooKeys 507: 41-97. https://doi.org/10.3897/zookeys.507.9536
All material examined and used for DNA barcoding: Explanation note: The dataset comprises all material examined and identified to a certain extent for this study. All specimens used for the descriptions of genus and listed species are included, as are all DNA barcoded specimens, including those that were published earlier.
Plant measurements and analytical results of direct and indirect iron deficiency of grapevine rootstocks
<p>Iron deficiency causes severe symptoms of leaf chlorosis with many crop species. In many cases the stess situation is induced by high lime stone content in soils. This study analyzed the response of grapevine rootstocks to no iron availability (-Fe) and a reduced iron availability (+Fe+BiC) with the aim to differentiate the response reaction. Plants were grown as woody cutting in pots filled with sand and fertilized with an half-strength Hoagland solution. Mesurements taken and data were obtained from samples collected at the end of the experiment after 4 weeks.</p>
SSR and SNP profiles obtained for 40 non-redundant grapevine genotypes found in the living collection of Ain Taoujdate (Morocco)
<p>This dataset includes the genetic profiles (13 SSR and 240 SNP markers) of 40 grapevine genotypes identified in the living collection of Ain Taoujdate (Morocco)</p>
Fig. 3 in Palaeogenomic insights into the origins of French grapevine diversity
Fig. 3 | Genetic origins of ancient and historic French grapevine varieties. Relationships identified between archaeological samples and modern cultivars included in the GrapeReSeq panel. Highly related refers to full-sibling or similar samples. Sibling relationships involving pairs of modern cultivar are not displayed for simplicity. Asterisks indicate archaeological seeds that were found consistent with carrying>10% paternal DNA. The VIVC (http://www.vivc. de) and GrapeReSeq identifiers for the modern cultivars can be found in Supplementary Table 4.
Fig. 2 in Palaeogenomic insights into the origins of French grapevine diversity
Fig. 2 | Geographical distribution and relationships between the distinct genetic types of archaeological samples. a, Relatedness among pairs of archaeological samples. Kinship coefficients were estimated using NgsRelate between pairs of samples for SNP loci present in the GrapeReSeq panel. The capital letters (A–F) on the left indicate genetically identical clones, that is, putative ancient and historical varieties. Asterisks indicate archaeological seeds that were found consistent with carrying>10% paternal DNA. b, Map displaying the distribution of genetic types (circles) in each archaeological site. The capital letters (A–F) on the circles indicate clusters of genetically identical seeds represented by more than one seed. The shading of the circles indicates sample age. In red is shown the genetic type that was found in more than one archaeological site. The lines connect pairs of samples that are related as parent–offspring or highly related/full sibling. Note that, as in the presence of paternal DNA full-sibling relationships could derive from multiple scenarios, we classified samples consistent with full-sibling relationships as 'highly related' (see Supplementary Methods 16).
Fig. 1 in Palaeogenomic insights into the origins of French grapevine diversity
Fig. 1 | Genetic affinities between archaeological grape seeds and modern V. vinifera accessions. a, MDS plot including archaeological samples, wild V. vinifera subsp. sylvestris accessions and domesticated varieties. b, MDS plot restricted to archaeological samples and domesticated varieties. The colours correspond to the main ancestry clusters identified in Laucou et al.21. Asterisks indicate archaeological samples that were incorporated into the data set by sampling a random allele from a majority count consensus sequence instead of called genotypes. c, Model-based clustering analysis of the GrapeReSeq panel assuming K = 8 clusters. The vertical bars represent individual accessions, the colours represent the inferred ancestry components and the fraction of each colour corresponds to the estimated ancestry proportion. Archaeological samples are sorted by age and by sample identification within a stratigraphic context. Samples that were identified as identical clones are grouped with black lines and capital letters (A–F) at the bottom.
The population genetics of structural variants in grapevine domestication
<p><strong>The genome assembly: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.fa.fasta?versionId=86a512b8-12a6-4f4d-ac5d-acc26d74589f">Chardonnay.fa.fasta</a> </p> <p><strong>The gene annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_sorted.gff.gz?versionId=2e5878bc-cf53-489b-ac71-2602f9ba4d2e">Chardonnay.annotation_sorted.gff.gz</a></p> <p><strong>The TE annotation: </strong><a href="https://zenodo.org/api/files/988c0749-aec9-42fe-865e-b09b140e2068/Chardonnay.annotation_te_sorted.gff3.gz?versionId=95780497-e0e7-4a7b-8860-74072d7f7bb2">Chardonnay.annotation_te_sorted.gff3.gz</a></p>
Fig. 1 in First Record of Ambrosiophilus atratus (Eichhoff, 1875) and Further Observations of Xylosandrus germanus (Blandford, 1894) (Coleoptera: Curculionidae: Scolytinae) on Grapevine, Vitis vinifera L. (Vitaceae)
Fig. 1. Live Ambrosiophilus atratus adult found boring into grapevine trunk in Pieve di Soligo, Veneto, Italy (April
Fig. 2 in First Record of Ambrosiophilus atratus (Eichhoff, 1875) and Further Observations of Xylosandrus germanus (Blandford, 1894) (Coleoptera: Curculionidae: Scolytinae) on Grapevine, Vitis vinifera L. (Vitaceae)
Fig. 2. SEM images of an Ambrosiophilus atratus adult extracted from grapevine trunk. A) Dorsal view, B) Lateral view.
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OpenNeuro
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