Persistent Identifier
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doi:10.57745/DV2X0M |
Publication Date
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2023-02-28 |
Title
| Gene sequence variation data for 3407 adult individuals from 164 range-wide populations of 7 widely distributed European forest tree species |
Point of Contact
|
Use email button above to contact.
Fady, Bruno (INRAE)
Pyhäjärvi, Tanja (University of Helsinki)
Kastally, Chedly (University of Helsinki) |
Author
| Pyhäjärvi, Tanja (University of Helsinki) - ORCID: 0000-0001-6958-5172
Bagnoli, Francesca (CNR)
Budde, Katharina (University of Göttingen) - ORCID: 0000-0002-5361-2815
Cavers, Stephen (CEH) - ORCID: 0000-0003-2139-9236
Cervantes, Sandra
Dauphin, Benjamin (WSL) - ORCID: 0000-0003-0982-4252
Fady, Bruno (INRAE) - ORCID: 0000-0003-2379-7617
Faivre-Rampant, Patricia (INRAE)
González-Martínez, Santiago (INRAE) - ORCID: 0000-0002-4534-3766
Grivet, Delphine (CSIC) - ORCID: 0000-0001-8168-4456
Gügerli, Felix (WSL) - ORCID: 0000-0003-3878-1845
Jorge, Véronique (INRAE) - ORCID: 0000-0002-5016-3006
Kastally, Chedly (University of Helsinki) - ORCID: 0000-0002-1820-4752
Lascoux, Martin (Uppsala University) - ORCID: 0000-0003-1699-9042
Lesur Kupin, Isabelle (INRAE) - ORCID: 0000-0001-7632-3955
Milesi, Pascal (Uppsala University) - ORCID: 0000-0001-8580-4291
Ojeda, Dario (NIBIO) - ORCID: 0000-0001-8181-4804
Olsson, Sanna (CSIC) - ORCID: 0000-0002-1199-4499
Opgenoorth, Lars (University of Marburg) - ORCID: 0000-0003-0737-047X
Pinosio, Sara (CNR) - ORCID: 0000-0002-1820-3637
Plomion, Christophe (INRAE) - ORCID: 0000-0002-3176-2767
Rellstab, Christian (WSL) - ORCID: 0000-0002-0221-5975
Rogier, Odile (INRAE) - ORCID: 0000-0001-6879-364X
Scalabrin, Simone (IGA Technology Services) - ORCID: 0000-0001-8686-8385
Scotti, Ivan (INRAE) - ORCID: 0000-0002-8951-2680
Vendramin, Giovanni G (CNR) - ORCID: 0000-0001-9921-7872
Westergren, Marjana (GOZDIS) - ORCID: 0000-0002-4204-0161 |
Distributor
| Entrepôt-Catalogue Recherche Data Gouv |
Description
| General description This dataset contains the targeted gene sequence variation data (vcf files and their tbi index files) of seven forest tree species used in the manuscript "Synchronous effective population size changes and genetic stability of forest trees through glacial cycles". The targeted genomic regions consisted of orthologous genes from putative functions involved in local adaptation, tolerance to drought and cold, leaf phenology, etc., as well as species-specific candidate genes and randomly selected genes. For each species, between 411 and 651 genotyped trees are included, sampled across their European range in at least 19 locations. Several versions are provided.
Species included: Pinus sylvestris, Picea abies, Fagus sylvatica, Populus nigra, Quercus petraea, Pinus pinaster, Betula pendula
Version descriptions v.5.3: Original SNP dataset, with samples and SNPs with poor coverage or other low quality removed, organelle contigs removed (described in the SNP filtering part of the manuscript), P. nigra clones and cultivars removed, and individuals mistakenly identified as the target species removed.
v.5.3.1: Master dataset derived from v.5.3, without samples with incorrect taxon assignment as indicated by genetic analysis for F. sylvatica and Q. petraea, identical to v.5.3 for the other five species.
v.5.3.2: Identical to v.5.3.1 but excludes P. abies samples from populations RU_PA_19, RU_PA_20 and RU_PO.
v.6.3.1: identical to v.5.3.1 but includes only four-fold degenerate sites, intron and intergenic sites, and only SNPs in low LD (1 kb windows, r < 0.5, PLINK v.1.90b4.9)
v.6.3.2: identical to v.6.3.1 but excluding singletons. Note that this version is in the .ped format and each file has their accompanying .map files with locus information.
English (2023-01-02) |
Subject
| Earth and Environmental Sciences; Medicine, Health and Life Sciences |
Data Type
| Dataset |
Related Publication
| Synchronous effective population size changes and genetic stability of forest trees through glacial cycles, by Milesi et al., 2023 (submitted). |
Related Dataset
| Michotey, Célia; Scalabrin, Simone; Pinosio, Sara; Aravanopoulos, Filippos A.; Brodbeck, Sabine; Cremer, Eva; Danusevicius, Darius; Donnelly, Kevin; González-Martinez, Santiago; Grivet, Delphine; Heer, Katrin; Jorge, Veronique; Milesi, Pascal; Pyhajarvi, Tanja; Vendramin, Giovanni; Fady, Bruno, 2021, "Genotyping dataset for 12 European forest tree species from H2020 project GenTree", https://doi.org/10.15454/7COC1A, Recherche Data Gouv, V1: doi: 10.15454/7COC1A |
Funding Information
| European Union’s Horizon 2020 Research and Innovation Programme: 676876 |
Depositor
| Fady, Bruno |
Deposit Date
| 2023-01-02 |