Quercus lobata Assembly and Gene Annotation

About Quercus lobata

Quercus lobata is a white oak of the Fagaceae family that is native to the interior of California, North America. It is a diploid species (2n=2x=24) with an estimated genome size of ∼730 Mbp. Mature specimens can grow up to 600 years. Valley oaks are important to California’s diverse Native American communities and their cultures, including influencing historic trade routes, and location of settlements. Its wood is used in cabinetry and hardwood flooring.

The Valley Oak Genome Project is an over-arching research program centered on an NSF-funded partnership between UCLA and Johns Hopkins University.

Assembly

ValleyOak3.0 is a diploid assembly of Quercus lobata isolate SW786. More details will be posted upon publication of the paper describing this assembly.

Annotation

Gene annotation was provided by valleyoak.ucla.edu. More details will be posted upon publication of the paper describing this assembly.

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 2,312,761 Low complexity (Dust) features, covering 74 Mb (8.8% of the genome); 231,802 RepeatMasker features (with the nrTEplants library), covering 87 Mb (10.2% of the genome); 752,294 Tandem repeats (TRF) features, covering 99 Mb (11.6% of the genome); Repeat Detector repeats length 379Mb (44.8% of the genome).

• First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae).
  Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL, Salzberg SL.. G3 (Bethesda) 6 (11)

Picture credit: https://www.wikiwand.com/en/Quercus_lobata

More information

General information about this species can be found in Wikipedia.