TreeGenes
Names
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TreeGenes
metasource: Fairsharing.org
version: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
A forest tree genome database
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Dendrome
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
TreeGenes
metasource: Fairsharing.orgversion: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
A forest tree genome database
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Dendrome
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Other names: A forest tree genome database, Dendrome
Names
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TreeGenes
metasource: Fairsharing.orgversion: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
A forest tree genome database
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Dendrome
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
TreeGenes is focused on connecting genomic, phenotypic, and environmental data for forest tree populations across the world. The database provides a custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The TreeGenes database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools.
Description
More detailed information about this field from each metasource.
TreeGenes is focused on connecting genomic, phenotypic, and environmental data for forest tree populations across the world. The database provides a custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The TreeGenes database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools.
metasource: Fairsharing.orgversion: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
TreeGenes is a genomic, phenotypic, and environmental data resource for forest tree species. The TreeGenes database and Dendrome project provide custom informatics tools to manage the flood of information.The database contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools. GMOD GUI tools such as CMAP for genetic maps and GBrowse for genome and transcriptome assemblies are implemented here. A sample tracking system, known as the Forest Tree Genetic Stock Center, sits at the forefront of most large-scale projects. Barcode identifiers assigned to the trees during sample collection are maintained in the database to identify an individual through DNA extraction, resequencing, genotyping and phenotyping. DiversiTree, a user-friendly desktop-style interface, queries the TreeGenes database and is designed for bulk retrieval of resequencing data. CartograTree combines geo-referenced individuals with relevant ecological and trait databases in a user-friendly map-based interface. ---- The Conifer Genome Network (CGN) is a virtual nexus for researchers working in conifer genomics. The CGN web site is maintained by the Dendrome Project at the University of California, Davis.
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Webpage:
https://treegenesdb.org/Webpage
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https://treegenesdb.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Licence:
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other
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Licence URL
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https://treegenesdb.org/
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Publications:
Publications
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TreeGenes: A forest tree genome database
PMID: 18725987
metasource: Fairsharing.org
version: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
TreeGenes: A forest tree genome database
PMID: 18725987
metasource: Fairsharing.org
version: FAIRsharing.org: TreeGenes; TreeGenes; DOI: https://doi.org/10.25504/FAIRsharing.lCVfCv; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
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TreeGenes: A forest tree genome database
PubMed citations: 36.
36 articles citing: TreeGenes: A forest tree genome database
Repetitive Elements, Sequence Turnover and Cyto-Nuclear Gene Transfer in Gymnosperm Mitogenomes. PMID:35692831
Genome-wide identification and characterization of Fusarium circinatum-responsive lncRNAs in Pinus radiata. PMID:35264109
Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. PMID:34897859
Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. PMID:34322154
Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge. PMID:34063405
The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant-specific motif. PMID:33236982
Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. PMID:32621602
Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. PMID:32546502
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Whole-proteome tree of life suggests a deep burst of organism diversity. PMID:32019884
275 years of forestry meets genomics in Pinus sylvestris. PMID:31988655
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
Genomics: cracking the mysteries of walnuts. PMID:31204723
The Road to Resistance in Forest Trees. PMID:31001287
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Growing and cultivating the forest genomics database, TreeGenes. PMID:30239664
Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation). PMID:30139335
Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis. PMID:27901510
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae). PMID:27387485
An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers. PMID:27190138
Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. PMID:26652261
Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom. PMID:26416765
MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants. PMID:24854168
Why assembling plant genome sequences is so challenging. PMID:24832233
The redox-sensitive chloroplast trehalose-6-phosphate phosphatase AtTPPD regulates salt stress tolerance. PMID:24800789
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. PMID:24647006
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource. PMID:24119028
Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PMID:24023741
Open access to tree genomes: the path to a better forest. PMID:23796049
Tripal: a construction toolkit for online genome databases. PMID:21959868
EuroPineDB: a high-coverage web database for maritime pine transcriptome. PMID:21762488
An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. PMID:21269494
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. PMID:20609256
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snps
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
bioinformatics
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genetic maps
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genome assembly
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
phenomics
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
phenotypics
metasource: re3data.org
version: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
snps
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
bioinformatics
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genetic maps
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genome assembly
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
phenomics
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
phenotypics
metasource: re3data.orgversion: re3data.org: TreeGenes; editing status 2021-09-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NQ19 last accessed: 2022-11-04
snps bioinformatics genetic maps genome assembly genomics phenomics phenotypics
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