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11 to 20 of 74 Results
May 9, 2019 - Omics Dataverse
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "Bioinformatic scripts to assess the effect of the cropping system on both community and network α- and β-properties of fungal microbiota", https://doi.org/10.15454/NSHUAQ, Portail Data INRAE, V1
These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/3DPFNJ. They are based on several softwares, including SparCC (Friedman and Alm 2012) and DADA2 (Callahan et al. 2016). The code corresponds to R and R markdown files. These scripts w...
Jun 28, 2019
Delye, Christophe, 2019, "R scripts and training data set for NGS-based resistance diagnosis", https://doi.org/10.15454/BCZF3S, Portail Data INRAE, V1, UNF:6:3whKFdlXAOan99XGTc9SSA== [fileUNF]
R scripts and training data set for NGS-based resistance diagnosis
Jul 2, 2019
Marais Colombel, Armelle, 2019, "Shallots virome", https://doi.org/10.15454/6XCMAE, Portail Data INRAE, V1
In order to elucidate the etiology of a novel disease on shallots in France, double-stranded RNAs from four symptomatic plants and two asymptomatic plants were analyzed using HTS. The disease has been characterized by foliar symptoms consisted of yellow stripes associated with a...
Jul 12, 2019 - Grapevine Downy Mildew Genomics Dataverse
Dussert, Yann; Gouzy, Jerome; Richart-Cervera, Sylvie; Mazet, Isabelle; Deliere, Laurent; Couture, Carole; Legrand, Ludovic; Piron, Marie-Christine; Bouchez, Olivier; Mestre, Pere; Delmotte, Francois, 2019, "Gene annotation of the Illumina draft of the Plasmopara viticola genome", https://doi.org/10.15454/NQEX46, Portail Data INRAE, V1
This dataset includes the gene annotation for the Illumina draft of the Plasmopara viticola genome. This genome draft has been published in Dussert et al. 2016 (doi.org/10.1128/genomeA.00987-16). The assembly can be found on GenBank (accession GCA_001695595.1).
Jul 12, 2019
Ma, Yuxin; Marais-Colombel, Armelle; Lefebvre, Marie; Svanella-Dumas, Laurence; Faure, Chantal; Candresse, Thierry, 2019, "Viral metagenomic data for comparison of two viral sequence enrichment approaches", https://doi.org/10.15454/TVWBCQ, Portail Data INRAE, V1
This study aims at comparing the performance of two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and Virion-associated nucleic acids (VANA) purification for the description of the viromes in various complex plant pools. In total 12 libraries were prepared for...
Jul 23, 2019
Leca, Alexandre, 2019, "Leaf wettability", https://doi.org/10.15454/2AVGI9, Portail Data INRAE, V1, UNF:6:6DOpNLa6g88wY+Y1TpNJoQ== [fileUNF]
This dataset contains wettability data in the form of contact angles measured on plant leaves. - First data provided are dynamic (advancing and receding) and receding (deposit and dropped) contact angles of water droplets on apple leaves (8 cultivars) and Parafilm 'M' (control su...
Jul 25, 2019
Ma, Yuxin; Marais, Armelle; Lefebvre, Marie; Faure, Chantal; Candresse, Thierry, 2019, "Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum", https://doi.org/10.15454/S486RR, Portail Data INRAE, V1
We selected tomato (Solanum lycopersicum) and european black nightshade (Solanum nigrum) as a pair of related crop-weed species to study the diversity and potential flow of viral populations using high throughput sequencing (HTS) based metagenomics. A total of 20 libraries were p...
Jul 25, 2019
Ma, Yuxin; Fort, Tania; Marais, Armelle; Lefebvre, Marie; Theil, Sebastien; Candresse, Thierry, 2019, "Viral metagenomic and fungal ITS metabarcoding data from complex pools of plant samples from southwestern France and for pools of fungal cultures obtained from these plant pools", https://doi.org/10.15454/X23KJF, Portail Data INRAE, V1
Using cross-disciplinary approaches to characterize the plant core microbiome, we assessed the diversity and composition of leaf-associated fungal and viral communities from composite samples of wild herbaceous plants in different ecological contexts. In total, 32 libraries were...
Jul 30, 2019 - Omics Dataverse
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "Amplicon Sequence Variant (ASV) table obtained by metabarcoding foliar fungal communities in conventional and organic vineyards", https://doi.org/10.15454/WOICSE, Portail Data INRAE, V1, UNF:6:PSwFBpb4Vxgr5rwUlkcPUQ== [fileUNF]
This Amplicon Sequence Variant (ASV) table was obtained by metabarcoding foliar fungal communities in conventional and organic vineyards. This table was generated after the application of the bioinformatics scripts (at https://doi.org/10.15454/NSHUAQ) to the sequences available a...
Jul 31, 2019
Ma, Yuxin; Marais, Armelle; Lefebvre, Marie; Faure, Chantal; Candresse, Thierry, 2019, "Supplementary tables to manuscript: “Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum”", https://doi.org/10.15454/RWOLLQ, Portail Data INRAE, V1, UNF:6:Mg1hXDjtGpQzxMfjXWjgyg== [fileUNF]
Supplementary tables to manuscript in Chapter 4
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