Genomic Resources

Valley Oak Genome v 3.0

This genome is our final assembly for Quercus lobata SW786.  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. The gene models are also available below, as well as other genomic resources.

You are welcome to use the genome and other resources. When using valley oak genome v3.0 and associated annotation, please cite:

V. L. Sork, S. J. Cokus, S. T. Fitz-Gibbon, A. Zimin, D. Puiu, L. Shiue, T. Swale, M. Pellegrini, S. L. Salzberg. https://valleyoak.ucla.edu/genomic-resources/ 

The manuscript is in prep:

V. L. Sork, S. J. Cokus, S. T. Fitz-Gibbon, A. Zimin, D. Puiu, J. A. Garcia, P. F. Gugger, L. Shiue, T. Swale, Y. Xhen, K. E. Lohmueller, M. Pellegrini, S. L. Salzberg. 2020. High-quality annotated genome and corresponding methylomes of a California oak provide new insights about the evolutionary success of the genus, Quercus
In prep.

Link to NCBI BioProject including access to raw sequence reads (2 PacBio & 11 Illumina libraries) — PRJNA308314

Download

Please note, some of the below analysis files were run on a version of the genome prior to deleting 18 scaffolds (identified to be derived from organelles) and replacing them with assembled versions: chrC, chrM1, chrM2 & chrM3.   See details below under “Organelle Contigs”.  Additionally 381,173 bps were converted to `N’s after being identified as inserted mis-assembly  of mitochrondrial sequence: inclusive-inclusive range chr1:[+]29726880..30108053.

Assembled Genome

GZIP’d Final Assembly, including 12 chromosomes, 2016 unplaced scaffolds, a complete chloroplast contig, and 3 mitochondrial contigs (~240MB) — Qlobata.v3.0.RptMsk4.0.6.on-RptMdl1.0.8.softmasked.fasta.gz

– RepeatMasker intervals and all Ns are lower case in the above file

GZIP’d Alternate Contigs  (from genomic regions where the two haplotypes assembled separately) (~117MB) — Qlobata.v3.0.alternateContigs.fasta.gz

Alternate Contigs extra information, sizes and relative coverage (~0.5MB) — Qlobata.v3.0.alternateContigs.info.txt

 

Protein Coding Gene Models, various formats

GZIP’d Gene Models, gtf format (~6.3MB) —  Qlobata.v3.0.PCG.gtf.gz

GZIP’d Gene Models, bed12 format (~2MB) — Qlobata.v3.PCG.bed.gz

GZIP’d Coding sequences (~13MB) — Qlobata.v3.0.PCG.CDS.fasta.gz

GZIP’d Protein sequences (~8MB) — Qlobata.v3.0.PCG.prot.fasta.gz

Protein Functional Names, via PANTHER (~2MB) Oak-NAMING-GENES.FIN1-viaPANTHER–V0-20200626.txt

If you download the genome sequence from NCBI, you may prefer this version of the gene model annotation, using NCBI contig names for chromosomes 1-12 (~6.3MB) — Qlobata.v3.0.PCG.NCBIchromosomeNames.gtf.gz

Gene Functions – InterProScan 5.34-73.0 run on 39,373 protein-coding gene models

GZIP’s TAR bundle of all IPS files listed below (~467 MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0–BUNDLE.tar.gz

– OR –

GZIP’d IPS GFF3 format (~17MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.gff3.gz

GZIP’d FASTA file with sequence fragments referred to from the GFF3 file (~15MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.gff3fasta.gz

GZIP’d IPS main tab-separated format (~10MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.tsv.gz

GZIP’d IPS active sites tab-separated format (~3MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.sites.tsv.gz

GZIP’d IPS XML format (~49MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.xml.gz

GZIP’d IPS JSON format (~49MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.json.gz

GZIP’d TAR archive of IPS HTML outputs per gene (~188MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.HTMLs.tar.gz

GZIP’d TAR archive of IPS SVG drawing per gene (~156MB) — Qlobata.v3.0.PCG.InterProScan5.34-73.0.SVGs.tar.gz

Orthologs – OMA Stand-alone version 2.3.1 run on Arabdopsis, Q. lobata, Q. robur & Q. suber

`ARATH’  (Arabidopsis thaliana: Ensembl Plants 38 TAIR10), `QueLo’ Quercus lobata (39,373 PCGs matching Sork et al. 2020 Figure 4A), `QueRo’ Quercus robur (25,808 PCGs matching Sork et al. 2020 Figure 4A), `QueSu’ Quercus suber (49,388 PCGs matching Sork et al. 2020 Figure 4A).

GZIP’s TAR (~45MB) — OMA2.3.1–ARATH-QueLo-QueRo-QueSu–BUNDLE.tar.gz

Repeats – RepeatModeler open-1.0.8 & RepeatMasker open-4.0.6

GZIP’d TAR archive of Repeat Modeler, full output (~573MB) — Qlobata.v3.0.RepeatModeler-open-1.0.8–BUNDLE.tar.gz

GZIP’d FASTA Repeat Modeler, consensi, passed to Repeat Masker (~0.5MB) — Qlobata.v3.0.RepeatModeler-open-1.0.8.consensi.fa.classified.gz

GZIP’d TAR archive of Repeat Masker full output, using above consensi file (~1.3GB) — Qlobata.v3.0.RptMsk4.0.6.on-RptMdl1.0.8–BUNDLE.tar.gz

GZIP’d UCSC BED6-format, Repeat Masker Repeat Families (~20MB) — Qlobata.v3.0.RptMsk4.0.6.on-RptMdl1.0.8.bed.gz

– the BED score column is 10 times the GFF file scores

– upper/lowercase of `RF:’/`rf:’ in BED column 4 follows as determined by RepeatMasker

GZIP’d list of Repeat Families combined to make each Super Family (~43KB) — Qlobata.v3.0.RptMsk4.0.6.on-RptMdl1.0.8.SFtoMemberFams.txt.gz

GZIP’d UCSC BED4-format Super Families (~14MB) — Qlobata.v3.0.RptMsk4.0.6.on-RptMdl1.0.8.SF.bed.gz

Repeats – LTR Harvest & LTR Digest from GenomeTools v.1.5.9

GZIP’s GFF listing LTR transposable elements — Qlobata.v3.0.QLz.LTRharvest-LTRdigest-1.5.9.gff.gz

 

RNAseq

raw reads and gene counts – bud, leaf & stem

 

PacBio RNA Sequencing (IsoSeq)

raw or polished reads and aligned contigs – bud, leaf & stem

 

Methylation – whole genome bisulfite sequencing, methylpy output (see https://pypi.org/project/methylpy/)

GZIP’d methylpy output, bud CG (~MB) — allc_bud.CG.tsv.gz

GZIP’d methylpy output, bud CHG (~MB) —  allc_bud.CHG.tsv.gz

GZIP’d methylpy output, bud CHH (~MB) — allc_bud.CHH.tsv.gz

GZIP’d methylpy output, catkin CG (~MB) — allc_catkin.CG.tsv.gz

GZIP’d methylpy output, catkin CHG (~MB) — allc_catkin.CHG.tsv.gz

GZIP’d methylpy output, catkin CHH (~MB) — allc_catkin.CHH.tsv.gz

GZIP’d methylpy output, youngLeaf CG  (~MB) — allc_youngLeaf.CG.tsv.gz

GZIP’d methylpy output, youngLeaf CHG (~MB) — allc_youngLeaf.CHG.tsv.gz

GZIP’d methylpy output, youngLeaf CHH (~MB) — allc_youngLeaf.CHH.tsv.gz

-raw fastq files are being submitted to NCBI.  A link will be posted ASAP. June 29 2020.

 

[Resequencing data for demography]

variants, aligned bam files (including unmapped reads) – will be posted by early July 2020.

 

Organelle Contigs

Some of the above analysis files were run on a version of the genome prior to deleting 18 scaffolds deemed organelle derived and replacing them with the following contigs.   These organelle contigs, ChrC, ChrM1, ChrM2 & ChrM3, are also included in the full genome download: Qlobata.v3.0.fasta.gz

GZIP’d FASTA chloroplast (1 contig, 161,289 bp) — Qlobata.v3.0.chloroplast.fasta.gz

GZIP’d GFF chloroplast (~3KB) — Qlobata.v3.0.chloroplast.gff.gz

GZIP’d FASTA mitochondrion (3 contigs, 444,512 bp) — Qlobata.v3.0.mitochondrion.fasta.gz

Scaffolds removed: Scq3eQI_83 Scq3eQI_674 Scq3eQI_14 Scq3eQI_18 Scq3eQI_787 Scq3eQI_1688 Scq3eQI_1766 Scq3eQI_789 Scq3eQI_1489 Scq3eQI_1288 Scq3eQI_972 Scq3eQI_771 Scq3eQI_795 Scq3eQI_672 Scq3eQI_1050 Scq3eQI_978 Scq3eQI_839 Scq3eQI_997)

 

Browser view of genomic resources of Q. lobata

Link to live browser will be posted by early July 2020.

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