Genomic Resources

Valley Oak Genome 3.0

This is our final assembly.  It includes 96% of the sequence in twelve chromosome length scaffolds labeled chr1, chr2,.. chr12.  There are an additional 2,016 unplaced scaffolds ordered by size and ranging from 1411,17 to 1001 bps.

We are working on annotation for version 3.0 and will post it as soon as completed.  In the meantime we will soon transfer our previous (crude) annotation to version 3.0 for temporary use.  Contact us if you would like to use this.

The new assembly is available on our ftp site at: ftp://ftp.ccb.jhu.edu/pub/dpuiu/Valley_oak/v3.0/

as FASTA contigs: ftp://ccb.jhu.edu/pub/dpuiu/Valley_oak/v3.0/oak_1Aug2018.fa.gz

and alternate: ftp://ccb.jhu.edu/pub/dpuiu/Valley_oak/v3.0/oak_14Aug2017.alternate.fa.gz

Chloroplast FASTA: ftp://ccb.jhu.edu/pub/dpuiu/Valley_oak/v3.0/chloro.fa

Mitochondrion FASTA: ftp://ccb.jhu.edu/pub/dpuiu/Valley_oak/v3.0/mito.fa

NCBI:  accession # LRBV00000000
Live browser coming soon...

Browser view of genomic resources of Q. lobata

Figure 3.  Snapshot of 50 Kbp (0.71 to 0.76 Mbp) from chromosome 1 of Q. lobata showing various genomic resources: dispersed and simple repeats, many tracks related to ongoing gene modeling (current consensus transcript models, PacBio long Iso-Seq transcripts, Illumina short RNA-Seq reads, Trinity-assembled RNA-Seq transcripts, AUGUSTUS predictions, aligned Q. robur and Q. suber proteins), and 5mC DNA cytosine methylation in one of our tissues (buds).

 

Valley Oak Genome 2.0

This consists of our scaffolds and contigs prior to
Dovetail scaffolding, i.e. our Hybrid+Transcript
Primary Merged assembly.

download

Valley Oak Genome 1.0

This assembly has been haplotype reduced by standard methods, however due to the high heterozygosity as much as a third of the genome is represented by both haplotypes. We expect coverage to be near complete.
-Valley Oak Genome 1.0 FASTA file download

– Valley Oak Genome 1.0 GFF file download
UCSC Genome Browser for Quercus lobata
Using the USCS Genome Browser Wiki

Annotation Methods
Currently annotations are only available for genome versions 0.5 and  1.0  and are of draft quality only!  We used MAKER (Campbell et al. 2014) to identify gene models and predict functional annotations in version 1.0, and then transferred those annotations to version 0.5 using the default pipeline of FLO (https://github.com/wurmlab/flo), which is based on the UCSC-Kent. Toolkit {Kuhn, 2012}. The liftover was successful for 43,864 (71%) of the 61,773 gene models.

Valley Oak Genome 0.5

This assembly has been aggressively haplotype reduced, resulting in very few genome regions represented more than once, but also approximately 100 Mb missing entirely. Due to high heterozygosity, typical assembly methods fail to collapse haplotypes for as much as half of the genome. We’ve found this version of the genome to be particularly useful as a reference genome for variant calling.
-Valley Oak Genome 0.5 (reduced) FASTA file download
-Valley Oak Genome 0.5 annotation gff file download
-SNPs and SMVs at Dryad