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TreeGenes specifications


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


  • person_outline David Neale

Publications for TreeGenes

TreeGenes citations


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

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 […]


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

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 (; last accessed April 25, 2017). These data are fragmented and redundant, as they have been generated by different technologies and experiments (, on […]


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

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 ( containing 18 253 sequences. The search parameters were as follows: a mass tolerance of 0.1 Da […]


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

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 (, last accessed April 6, 2016) and the Congenie website (, last […]


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

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

[…] In addition, the protein sequences of Gymnospermae species, including P. taeda, P. sitchensis and P. abies, were downloaded from the Forest Tree Genome database (, and the sequences of the other 38 species used in this study were downloaded from JGI ( All of these species are representative species of the different branche […]


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

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 […]


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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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