Summary
Publication
Plomion C, Aury JM, Salse J. Oak genome reveals facets of long lifespan. Nature Plants. 2018 June 18; volume 4, (2018) :440–452.
Name
Quercus robur - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
Blaster, Censor, RepeatMasker
Program Version
v.26.0
Date Performed
Tuesday, November 13, 2018 - 15:44
Data Source
Description and Download
An Invisorb Spin Plant Mini Kit (Stratec Molecular) was used to isolate genomic DNA and prepare short-read libraries for the Roche-454 and Illumina sequencing platforms. DNA concentrations were determined using a Quant-iT dsDNA Assay Kit (Life Technologies) and a Qubit Fluorometer (Invitrogen). Agarose-embedded high-molecular weight (HMW) DNA was prepared to construct Illumina TruSeq Synthetic Long Read (TSLR) libraries. DNA concentrations were quantified with the Quant-iT dsDNA Assay Kit. DNA quality was then checked using an Argus Qcard Kit (OpGen) and was estimated at 20–100 kb. 454 single-end read libraries according to the standard procedure provided by Roche, with RL adaptors (GS FLX Titanium Rapid Library Preparation Kit; Roche Diagnostic). The libraries were sequenced with titanium chemistry on a 1/2 Pico Titer Plate on a 454 GS FlX instrument (Roche Diagnostic). Longest reads were assembled together (obtained from 454 and Moleculo libraries) to maximize the separation of the two haplotypes of accession 3P and to overcome the high level of heterozygosity. An assembly of 300,113 contigs with an N50 of 9.3 kb and a cumulative size of 1.31 Gb, corresponding roughly to the size of the two haplotypes.

Downloads

Version PM1N
Haploid version: 12 pseudomolecules with 871 scaffolds + 538 unassigned scaffolds Genomic scaffolds
All Gene Models CDS
All Gene Models Protein
All Gene Models GFF
Version V2
Diploid version 2 Genomic scaffolds
Version V1
Diploid version 1 from Plomion et al. 2016 Mol Ecol Res 16: 254-265 Genomic scaffolds
For more information please see the Quercus Genome Site
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