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Icon 02 Links

Conifer Genome Network PineRefSeq Project SMarTForests Project Conifer Translational Genomics Network TreeGenes Database Dendrome Plone Forestry Careers and Education Resource



Browser Portal

Currently, TreeGenes uses two web based browsers for sequence and annotation visualization. First, the Generic Genome Browser (GBrowse v. 2.54) is a combination of database and interactive website for manipulating and displaying annotations on genomes.

The second browser, WebApollo (In progress...) (v. 052013), is built upon JBrowse. From WebApollo, a variety of annotation tracks are available for visualization against the draft assembly of the Loblolly Pine ( Pinus taeda ) genome.

GENOME
Betula nana | Alpine Birch | Bena
VersionStatsData UseMoreProject Page
1.0 Statistics Citation Genome v1.0[Birch Genome] Dwarf Birch Genome Project
Betula nana ENA (SAME2271942)
Eucalyptus camaldulensis | Murray Red Gum | Euca
VersionStatsData UseMoreProject Page
1.0 Statistics Citation Genome v1.0 Eucalyptus camaldulensis Genome Database
Eucalyptus camaldulensis at DNA Data Bank of Japan
Eucalyptus grandis | Rose Gum | Eugr
VersionGbrowseStatsData UseProject Page
1.1 Genome v1.1 Statistics Citation Eucalyptus grandis v1.1 at Phytozome
Eucalyptus grandis BioSample (NCBI SAMN02851740)
Fraxinus excelsior | European Ash | Frex
VersionStatsData UseMoreProject Page
0.4 Statistics Data Use Policy Genome v0.4[Ash Genome]
Fraxinus excelsior BioSample (NCBI SAME3138923)
Julgans regia | English Walnut | Reju
Version Browsers Stats Data Use Project Page
1.0 JBrowse Statistics Data Use Policy Walnut Genomics Implementation Group
Juglans regia BioProject (NCBI 291087)
Manihot esculenta | Cassava | Maes
VersionBrowsers Stats Data Use Project Page
6.1 Manihot esculenta 6.1 at Phytozome
4.1 GBrowse Statistics Citation Manihot esculenta 4.1 at Phytozome
1.1 GBrowse
Picea abies | Norway Spruce | Paab
Version Stats Data Use More Project Page
1.0 Approximately 20 Gb Citation Assembly v1.0[Congenie] Spruce Genome Project
Picea glauca | White Spruce | Pagl
Version Stats Data Use More Project Page
1.0 Statistics Citation White Spruce Genome Sequence Assembly (v3)
Genomic Scaffolds v3.0
SMarTForests
Picea glauca at ENA (SAMN01120252)
Pinus lambertiana | Sugar Pine | Pila
Version Stats Data Use More Project Page
1.0 Statistics Data Use Policy Mito PineRefSeq Project
Pinus lambertiana BioProject 9NCBI 31033)
0.5 Statistics
Pinus taeda | Loblolly Pine | Pita
Statistics
Version Browsers Stats Data Use Project Page
1.01 GBrowse
WebApollo
login:demo, password:demo
Statistics Citations: Neale et al, Zimin et al., Wegrzyn et al, Wegrzyn et al. PineRefSeq Project

Pinus taeda BioProject (NCBI PRJNA174450)
1.0 Statistics
0.8
0.6 Statistics
Populus tremula | European Aspen | Pota
Version JBrowse Stats Data Use Project Page
1.0 Genome v1.0 Approximately 210,683 contigs Citation
Data Use Policy
Popgenie
Populus tremula x Populus tremuloides | Potl
Version Browsers Stats Data Use Project Page
0.1 JBrowse Approximately 290,142 contigs Data Use Policy Popgenie
P. tremula x P. tremuloides EST BioProject (NCBI 13256)
Populus tremuloides | Trembling Aspen | Pote
Version Browsers Stats Data Use Project Page
1.0 JBrowse Approximately 184,651 contigs Data Use Policy Popgenie
Populus trichocarpa | Black Cottonwood | Potr
Version Browsers Stats Data Use Project Page
3.0 GBrowse Statistics Citation Popgenie
Populus trichocarpa v3.0 (Western Popular)
2.2 GBrowse
1.1
Pseudotsuga menziesii | Douglas-Fir | Psme
Version Stats Citation More Project Page
0.5 Statistics Data Use Policy PineRefSeq Project
Quercus robur | English Oak | Quro
Version Stats Data Use Project Page
1 Statistics Citation Oak Genome Sequencing Project
Quercus robus BioProject (NCBI 285761)
Quercus robus genome sequencing (ENA PRJEB7855)
Vitis Vinifera | Grape | Vivi
Version Browsers Stats Data Use Project Page
12X JBrowse 487Mb arranged in 19 chromosomes Citation Grape Genome Browser
Vitis vinifera at Phytozome
TRANSCRIPTOME
Picea abies
Picea engelmannii x Picea glauca
Transcriptome v1.0 - 16,069 contigs
Picea glauca
Picea mariana
Transcriptome v1.0 - 2,791 contigs
Picea sitchensis
Transcriptome v1.0 - 45,985 contigs
Pinus banksiana
Pinus contorta
Pinus lambertiana
Pinus palustris
Transcriptome v1.0 - 14,228 contigs
Pinus pinaster
Pinus radiata
Pinus sylvestris
Pinus taeda
Transcriptome v1.0 - 77,249 contigs annotated
Annotation Report v1.0
Populus tremula
Transcriptome v0.2 - 107,753 contigs annotated
Pseudotsuga menziesii
Transcriptome v1.0 - 51,548 contigs annotated

Icon 03 Updates

PineRefSeq project releases assembly (v2.0) of the Pinus taeda genome Walnut genome project releases assembly (v1.0) of the Juglans regia genome PineRefSeq project releases assembly (v1.0) of the Pseudotsuga menziesii genome PineRefSeq project releases assembly (v1.0) of the Pinus lambertiana genome CartograTree (v3.0), a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! PineRefSeq project releases assembly (v1.01) of the Pinus teada genome SMarTForests Project releases the third assembly of the Picea glauca genome

Icon 01 Events

UK Plant Evolution 2016 meeting

Cambridge University, UK
September 15-16, 2016
2nd Annual Meeting in Conservation Genetics – From Research to Applications

Tagungszentrum an der Sternwarte, Germany
October 5-6, 2016
PAG XXV

San Diego, CA, USA
January 14-18, 2017

Icon 04 Contact

tg-help@ucdavis.edu

Icon 03 Connect