Summary
Resource Type
Organism
Abbreviation
Q. robur
Genus
Quercus
Species
robur
Common Name
Pedunculate Oak
Organism Image
Cross Reference
Description
Other Common Names: English Oak Order: Fagales Family: Fagaceae Chromosome Number: 2n=24 Genome Size: 740 Mbp Links to other sites housing genomic resources: BAC Library (available from the CNRGV) Transcriptome Sequences (available from the Quercus Portal) Densely Populated Genetic Map (available from the Quercus Portal) Quercus Portal - a european genetic and genomic web resource for Quercus Draft Reference Genome: A French consortium led by Christophe Plomion at INRA Bordeaux has sequenced and assembled the Q. robur genome. Oak Genome Sequencing Website Publication: Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse S, Quesneville H, Kremer A (2016) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Res. 16: 254-265
Reference Genome
NameProgramDate Constructed
Quercus robur - Reference GenomeBlaster, Censor, RepeatMaskerNov 13th, 2018
JBrowse

JBrowse instance corresponds to Quercus robur reference genome assembly.

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Analysis Details
Provides detailed information on the programs used to assemble and annotate the data.
NameProgramDate Constructed
Oak gene expression atlasDESeqJan 15th, 2020
Quercus robur df159DESeq2Feb 10th, 2020
Quercus robur Gene AtlasNextflow Gene Expression (Skewer, STAR, HTSeq)Mar 9th, 2020
Quercus robur - peptides KEGGkegg (Ghost Koala) Jul 19th, 2019
Quercus robur - Reference GenomeBlaster, Censor, RepeatMaskerNov 13th, 2018
Quercus robur - mRNA BLASTX against SwissProtblastxNov 16th, 2018
Quercus robur - mRNA BLASTX against TrEMBLblastxNov 16th, 2018
Quercus robur peptides InterProScaninterproscanNov 16th, 2018
Biological Samples
NameTissueTreatmentDescription
ERS1566595Not setNot setsample_BHD_38942
ERS1444872Not setNot setsample_BHD_38865
FK48Lateral rootAcH_505 P_croceumLateral roots stage D AcH_505 P croceum replicate 3
FK47LeafAcH_505 P_croceumLeaves stage D AcH_505 P croceum replicate 3
FK46ALateral rootAcH_505 P_croceumLateral roots stage D AcH_505 P croceum replicate 2
SRS2075407mycorrhizal root tipsNot setTubma_Qrob_mycorrhiza 1
SRS2075406mycorrhizal root tipsNot setTubma_Qrob_mycorrhiza 2
SRS2075408mycorrhizal root tipsNot setTubma_Qrob_mycorrhiza 3
SRS2075409mycorrhizal root tipsNot setTubae_Qrob_mycorrhiza 1
SRS2075410mycorrhizal root tipsNot setTubae_Qrob_mycorrhiza 2

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Libraries
NameTypeStatus
Quercus robur HindIII BAC Librarynucleic_acid_librarycurrent
Quercus robur EcoRI BAC librarynucleic_acid_librarycurrent
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