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1 to 10 of 15 Results
Jul 16, 2020
Fort, Tania; Pauvert, Charlie; Zanne, Amy; Ovaskainen, Otso; Caignard, Thomas; Barret, Matthieu; Compant, Stéphane; Hampe, Arndt; Delzon, Sylvain; Vacher, Corinne, 2020, "Bioinformatic and statistical scripts to analyze metabarcoding data of fungal communities", https://doi.org/10.15454/0CNFWS, Portail Data INRAE, V1, UNF:6:AbAHJCHSVEP+kwY2z9TN7A== [fileUNF]
This dataset contains R-scripts to analyse the diversity and composition of seed fungal communities (Fort et al., Maternal effects shape seed fungal communities in Quercus petraea. Submitted). The bioinformatic script was applied to raw sequences after paired-end sequences were j...
Mar 24, 2020 - Biogeco Dataverse
Dutech, Cyril; Feau, Nicolas; Lesur, Isabelle; Ehrenmann, François; Letellier, Thomas; Li, Bayo; Mouden, Charlotte; Guichoux, Erwan; Desprez-Loustau, Marie-Laure; Gross, Andrin, 2020, "An easy and robust method for isolation and validation of single nucleotide polymorphic markers from the Erysiphe alphitoides, the oak powdery mildew, draft genome", https://doi.org/10.15454/UGMTBK, Portail Data INRAE, V2
This dataset includes the sequence and SNP data, and the scripts for detecting SNP from targeted sequences isolated from the Erysipe alphitoides draft genome. The draft genome sequencing used the SRR10956459 short reads (Bioproject: PRJNA593204). Assembly and Annotation of the dr...
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 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...
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 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 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).
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 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...
May 7, 2019
Pauvert, Charlie; Vallance, Jessica; Delière, Laurent; Buée, Marc; Vacher, Corinne, 2019, "DNA metabarcoding of foliar fungal communities in conventional and organic vineyards", https://doi.org/10.15454/3DPFNJ, Portail Data INRAE, V1
This sequence dataset (FASTQ format) was obtained by metabarcoding foliar fungal communities in conventional and organic vineyards. The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platfor...
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