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Eleanor
Smith
Life Sciences Librarian
919-513-3969
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Trees
general and comparative resources |
sequence
data by species: eucalyptus | pine | poplar | spruce | major
tree research centers and sources
General and Comparative Resources
Conifer Comparative Genomics Project (CCGP; University of
California, Davis)
http://dendrome.ucdavis.edu/ccgp/index.html
http://dendrome.ucdavis.edu/ccgp/sewell.html (pine
consensus map)
CCGP is focused on the development of genetic resources for comparative
genomic analysis in conifers. The site includes a consensus map for loblolly
pine (Pinus
taeda) and several comparative maps: Loblolly vs. Slash pine, Maritime
pine, Scots pine, and Douglas fir.
Dendrome, a Forest Tree Genomic Database (Department
of Environmental Horticulture
University of California, Davis)
http://dendrome.ucdavis.edu/
Dendrome maintains a collection of forest tree genome databases and other
forest genetic information resources. Some of the resources available through
Dendrome include:
- TreeGenes
http://dendrome.ucdavis.edu/treegenes/species/
TreeGenes is the primary genome database of Dendrome. TreeGenes provides curated
information about maps, sequences, markers, QTLs, and ESTs for several forest
tree species. There are around 70 genetic maps in TreeGenes.
- Dendrome Literature Database
http://dendrome.ucdavis.edu/treegenes/literature/
Dendrome maintains a comprehensive literature database related to forest tree
genetics. The database is updated bi-weekly and article information is obtained
from a number of public repositories.
Sequence Resources by Species
Species |
Data Type |
URL for Data/Databases |
Organization* |
Eucalyptus
|
ESTs |
Eucalyptus camaldulensis
Data hosted at BioData:
http://biodata.ccgb.umn.edu/
eucalyptus_camaldulensis/ |
ForBio: an Australian biotechnology company.
BioData: http://biodata.ccgb.umn.edu/ |
ESTs |
Eucalyptus globulus
Data hosted at BioData:
http://biodata.ccgb.umn.edu/
eucalyptus_globulus/ |
ForBio: an Australian biotechnology company.
BioData: http://biodata.ccgb.umn.edu/ |
Pine
(Pinus)
|
ESTs |
Loblolly Pine Pilot Project
Data hosted at BioData:
http://biodata.ccgb.umn.edu/ifgpine/ |
Institute of Forest Genetics of the USDA
Forest Service. BioData: http://biodata.ccgb.umn.edu/ |
ESTs |
NCSU Pine EST
Data hosted at BioData:
http://biodata.ccgb.umn.edu/ncsupine/ |
BioData http://biodata.ccgb.umn.edu/ |
ESTs |
Pine Gene Discovery
http://biodata.ccgb.umn.edu/doepine/
|
BioData http://biodata.ccgb.umn.edu/ |
ESTs |
Pine Gene Index (PGI)
http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=pine |
Computational Biology and Functional Genomics Laboratory,
Harvard University: http://compbio.dfci.harvard.edu/tgi/
|
Poplar
(Populus)
|
ESTs |
EST sequencing in Poplar
Data hosted at BioData:
http://biodata.ccgb.umn.edu/poplar/ |
Arborea
http://www.arborea.ulaval.ca/ |
ESTs |
Poplar Gene Index
http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=poplar |
Computational Biology and Functional Genomics Laboratory,
Harvard University:http://compbio.dfci.harvard.edu/tgi/ |
ESTs
|
PopulusDB
http://www.populus.db.umu.se/
|
Department of Plant Physiology, Umeå University,
Department of Forest Genetics and Plant Physiology, SLU Umeå, and
Department of Biotechnology, KTH Stockholm
http://www.populus.db.umu.se/ |
Gen-ome, func-tional annot. |
PoplarDB
http://mycor.nancy.inra.fr/poplardb/ |
Genome Initiative called LIGNOME at
INRA, The French National Institute for Agricultural Research
http://www.inra.fr/ |
Com-plete Gen-ome |
Populus trichocarpa v 1.0
http://genome.jgi-psf.org/Poptr1/
Poptr1.home.html |
Joint Genome Institute (JGI)
http://genome.jgi-psf.org/ |
Organ-elle |
Populus chloroplast analysis files
http://genome.ornl.gov/poplar_chloroplast
/poplar_chloroplast.html
|
Oak Ridge National Laboratory (ORNL)
http://genome.ornl.gov/ |
Spruce
|
ESTs |
EST sequencing in Spruce
Data hosted at BioData:
http://biodata.ccgb.umn.edu/spruce/ |
Arborea
http://www.arborea.ulaval.ca/
|
ESTs |
Spruce Gene Index
http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=spruce |
Computational Biology and Functional Genomics Laboratory,
Harvard University:http://compbio.dfci.harvard.edu/tgi/ |
*Note: Detailed descriptions of the organizations and their projects are
provided following the table.
Forest Tree Projects hosting Data for Multiple Tree
Species
Arborea (Faculty of Forestry and Geomatics,
Université Laval)
http://www.arborea.ulaval.ca/
One of the main activities of this tree genomics research project involves
large-scale sequencing of ESTs. Sequence information is available through the
databases SpruceDB and ForestTreeDB and the BioData webpages (developed in
partnership with the Center for Computational Biology and Genomics at the University
of Minnesota). Data are available from two projects:
- EST Sequencing in Spruce
http://biodata.ccgb.umn.edu/spruce/
Seventeen white spruce libraries were sequenced and 70,000 ESTs analyzed yielding
49,000 total quality reads. The cDNA libraries cover various organs, developmental
stages, and treatments. Unigenes, analysis, annotation, and an online database
are available.
- EST Sequencing in Poplar
http://biodata.ccgb.umn.edu/poplar
Poplar sequencing was carried out on 14,000 random cDNAs from 7 libraries
representing several tissues under various treatments. This resulted in over
11,000 quality reads. Sequences, sequence assemblies, and a database are available.
Biodata
System (CCGB; Center for Computational Genomics & Bioinformatics)
http://biodata.ccgb.umn.edu/
The Biodata system stores DNA sequence data from numerous research projects.
The sources below include data from forest tree projects. CCGB provides computing
and analysis resources to support the research of investigators at the University
of Minnesota. The links below include data from forest tree projects.
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