Genomic Resources

Valley Oak Genome 3.0

This is our final assembly.  It includes 96% of the sequence in twelve chromsome 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.

Valley Oak Genome 2.0

This consists of our scaffolds and contigs prior to

Dovetail scaffolding, i.e. our Hybrid+Transcript

Primary Merged assembly.


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


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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

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 (, which is based on the UCSC-Kent. Toolkit {Kuhn, 2012}. The liftover was successful for 43,864 (71%) of the 61,773 gene models.