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1 to 10 of 18 Results
Feb 26, 2020 - Grapevine Downy Mildew Genomics Dataverse
Dussert, Yann; Legrand, Ludovic; Mazet, Isabelle D.; Couture, Carole; Piron, Marie-Christine; Serre, Rémy-Felix; Bouchez, Olivier; Mestre, Pere; Toffolatti, Sylvia Laura; Giraud, Tatiana; Delmotte, François, 2020, "Data from: Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen, Plasmopara viticola", https://doi.org/10.15454/ILQ12T, Portail Data INRAE, V1
This dataset includes analysis files for the paper "Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen, Plasmopara viticola" submitted to bioRxiv (doi.org/10.1101/2020.02.26.962936). Archives can contain README files with import...
Feb 18, 2020
Vacher, Corinne, 2020, "R scripts used to infer microbial networks from metabarcoding data and validate them using text-mining", https://doi.org/10.15454/5WD6P6, Portail Data INRAE, V1, UNF:6:LNjhKptvEnA9T2eqRWfBNQ== [fileUNF]
R scripts and datafiles used to infer microbial association networks from metabarcoding data of grapevine foliar samples infected or not by powdery mildew (Erysiphe necator). R script used to search for microbial associations in the Scopus database.
Feb 18, 2020
Vacher, Corinne, 2020, "DNA metabarcoding of foliar fungal communities in an untreated vineyard", https://doi.org/10.15454/A24N4C, Portail Data INRAE, V1
This sequence dataset (FASTQ format) was obtained by metabarcoding fungal communities of 20-days old leaves in an untreated vineyard located in INRA Vilenave d'Ornon (France). The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pai...
Feb 7, 2020 - Grapevine Downy Mildew Genomics Dataverse
Couture, Carole, 2020, "http://grapevine-downy-mildew-genome.com/", https://doi.org/10.15454/U1VH0Z, Portail Data INRAE, V1
website about grapevine downy mildew genome
Feb 6, 2020 - Grapevine Downy Mildew Genomics Dataverse
Dussert, Yann; Couture, Carole; Mazet, Isabelle D.; Gouzy, Jérôme; Piron, Marie-Christine; Kuchly, Claire; Bouchez, Olivier; Rispe, Claude; Mestre, Pere; Delmotte, François, 2018, "Genome assembly and annotation of Plasmopara viticola, the grapevine downy mildew pathogen", https://doi.org/10.15454/4NYHD6, Portail Data INRAE, V4
This dataset includes the assembly and annotation of the Plasmopara viticola genome (INRA-PV221 isolate), following genome sequencing using PacBio long reads at deep coverage. The paper describing the genome is now published in Genome Biology and Evolution (doi.org/10.1093/gbe/ev...
Nov 15, 2019
Zemb, Olivier, 2019, "Absolute quantitation of microbes using 16S rRNA gene metabarcoding: a rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard", https://doi.org/10.15454/YWMMH4, Portail Data Inra, V1, UNF:6:F0zGeneCWQ7Kv1ouvU+bEQ== [fileUNF]
Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standar...
Sep 2, 2019
Pauvert, Charlie; Buee, Marc; Laval, Valérie; Edel-Hermann, Véronique; Fauchery, Laure; Gautier, Angélique; Lesur Kupin, Isabelle; Vallance, Jessica; Vacher, Corinne, 2018, "Bioinformatic scripts allowing the comparison of fungal metabarcoding pipelines", https://doi.org/10.15454/VKTWKR, Portail Data Inra, V4
This dataset contains scripts and code that can be used to compare metabarcoding pipelines using a fungal mock community. These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/8CVWRR (Pauvert et al. Bioinformatics matters: the accuracy o...
Jul 30, 2019
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 Inra, 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 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 Inra, 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).
May 9, 2019
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 Inra, 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...
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