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Protocols

TreeGenes specifications

Information


Unique identifier OMICS_32166
Name TreeGenes
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline David Neale

Publications for TreeGenes

TreeGenes citations

 (11)
call_split

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas fir needles

2017
BMC Genomics
PMCID: 5525293
PMID: 28738815
DOI: 10.1186/s12864-017-3916-y
call_split See protocol

[…] sembled for each individual, and the combined clustered reference assembly is provided in Additional file . Individual assemblies and the pan-transcriptome reference are available for download at the TreeGenes Forest Tree Genome database web site under the link “Pseudotsuga menziesii Transcriptome” [].To annotate plant-derived transcripts, we used BLASTX and TBLASTX [] to identify transcript match […]

library_books

Single Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

2017
Genome Biol Evol
PMCID: 5414570
PMID: 28460034
DOI: 10.1093/gbe/evx070

[…] We retrieved transcriptome data from another 25 gymnosperms that were stored in PlantGDB (), oneKP (), and TreeGenes (https://dendrome.ucdavis.edu/treegenes/; last accessed April 25, 2017). These data are fragmented and redundant, as they have been generated by different technologies and experiments (, on […]

library_books

Proteomic analysis of stress‐related proteins and metabolic pathways in Picea asperata somatic embryos during partial desiccation

2016
Plant Biotechnol J
PMCID: 5253475
PMID: 27271942
DOI: 10.1111/pbi.12588

[…] roteome Discoverer 1.2 (PD 1.2, Thermo, 5600 msconverter) and the files were searched. Proteins were identified using the Mascot search engine (Matrix Science, London, UK; version 2.3.02) against the TreeGenes nonredundant sequence database (http://dendrome.ucdavis.edu/treegenes/protein/prot_summary.php) containing 18 253 sequences. The search parameters were as follows: a mass tolerance of 0.1 Da […]

library_books

An Ancient Transkingdom Horizontal Transfer of Penelope Like Retroelements from Arthropods to Conifers

2016
Genome Biol Evol
PMCID: 4860704
PMID: 27190138
DOI: 10.1093/gbe/evw076

[…] The genomes of loblolly pine and Norway spruce were downloaded from the TreeGenes () ftp website (http://dendrome.ucdavis.edu/ftp/Genome_Data/genome/pinerefseq/Pita/transcriptome/, last accessed April 6, 2016) and the Congenie website (ftp://plantgenie.org/ConGenIE/, last […]

library_books

Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO like genes in plant kingdom

2015
Sci Rep
PMCID: 4586889
PMID: 26416765
DOI: 10.1038/srep14631

[…] su.edu/). In addition, the protein sequences of Gymnospermae species, including P. taeda, P. sitchensis and P. abies, were downloaded from the Forest Tree Genome database (http://dendrome.ucdavis.edu/treegenes/), and the sequences of the other 38 species used in this study were downloaded from JGI (http://www.phytozome.net/). All of these species are representative species of the different branche […]

call_split

Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource

2013
BMC Genomics
PMCID: 4007752
PMID: 24119028
DOI: 10.1186/1471-2164-14-702
call_split See protocol

[…] Processing of raw trace files was performed through the customized TreeGenes EST pipeline []. Base-calling and quality-assignment of the sequences were conducted with Phred (versions 0.000925.c and 0.020425.c) [,]. Low quality bases below Phred20 were masked and vect […]

Citations

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TreeGenes institution(s)
Department of Plant Sciences, University of California, Davis, CA, USA; Department of Evolution and Ecology, University of California, Davis, CA, USA
TreeGenes funding source(s)
Supported by NSF (1443040 and 1444573), USDA (2016-67013-24469).

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