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| Título: | Supplementary data for An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype |
Autor: | Velt, Amandine; Frommer, Bianca; Blanc, Sophie; Holtgräwe, Daniela; Duchêne, Éric; Dumas, Vincent; Grimplet, Jérôme CSIC ORCID; Hugueney, Philippe; Kim, Catherine; Lahaye, Marie; Matus, José Tomás CSIC ORCID CVN ; Navarro-Payá, David CSIC ORCID; Orduña, Luis CSIC ORCID; Tello-Ruiz, Marcela K.; Vitulo, Nicola; Ware, Doreen; Rustenholz, Camille | Fecha de publicación: | 2023 | Editor: | Oxford University Press | Citación: | Velt, Amandine; Frommer, Bianca; Blanc, Sophie; Holtgräwe, Daniela; Duchêne, Éric; Dumas, Vincent; Grimplet, Jérôme; Hugueney, Philippe; Kim, Catherine; Lahaye, Marie; Matus, José Tomás; Navarro-Payá, David; Orduña, Luis; Tello-Ruiz, Marcela K.; Vitulo, Nicola; Ware, Doreen; Rustenholz, Camille; 2023; Supplementary data for An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype [Dataset]; Oxford University Press; https://doi.org/10.1093/g3journal/jkad067 | Descripción: | Supplemental files are provided with the manuscript. Supplementary File 1 contains additional figures and Supplementary File 2 additional tables. Raw sequencing data and the PN40024.v4 genome assembly are available at ENA under BioProject PRJEB45423. Also, the PN40024.v4 genome assembly with structural and functional gene annotation is available on the INTEGRAPE website (https://integrape.eu/resources/genes-genomes/genome-accessions), on the Grape Genomics Encyclopedia portal (http://grapedia.org/) and under the DOI number doi:10.57745/F9N2FZ (https://entrepot.recherche.data.gouv.fr/dataset.xhtml?persistentId=doi:10.57745/F9N2FZ). A Sequence Server v2.0.0 interface (http://138.102.159.70:4567/) was set up to perform BLAST analyses. A JBrowse interface (http://138.102.159.70/jbrowse/) was set up to visualize PN40024.v4 assembly and PN40024.v4.1 and v4.2 annotations, but also some previous annotation versions that were transferred, some RNA-Seq alignments and miscellaneous tracks. An Apollo interface (http://138.102.159.70:8080/apollo; training and account mandatory) was set up to manually curate gene annotations according to the dedicated guidelines (https://integrape.eu/resources/data-management/). Code used to analyze GBS data can be found at https://forgemia.inra.fr/sophie.blanc/gbs and code used to generate the PN40024.v4.2 version can be found at https://gitlab.com/MSVteam/pn40024-visualization-tools/-/tree/master/update_gff3_script. Supplemental material available at G3 online. | URI: | http://hdl.handle.net/10261/334860 | DOI: | 10.1093/g3journal/jkad067 | Referencias: | Velt, Amandine; Frommer, Bianca; Blanc, Sophie; Holtgräwe, Daniela; Duchêne, Éric; Dumas, Vincent; Grimplet, Jérôme; Hugueney, Philippe; Kim, Catherine; Lahaye, Marie; Matus, José Tomás; Navarro-Payá, David; Orduña, Luis; Tello-Ruiz, Marcela K.; Vitulo, Nicola; Ware, Doreen; Rustenholz, Camille. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. https://doi.org/10.1093/g3journal/jkad067. http://hdl.handle.net/10261/334853 |
| Aparece en las colecciones: | (I2SysBio) Conjuntos de datos |
Ficheros en este ítem:
| Fichero | Descripción | Tamaño | Formato | |
|---|---|---|---|---|
| jkad067_supplementary_data.zip | 949,3 kB | Unknown | Visualizar/Abrir | |
| README.txt | 3,2 kB | Text | Visualizar/Abrir |
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