First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae)

Oaks represent a valuable natural resource across Northern Hemisphere ecosystems attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobate) using Illumina sequencing of adult leaf tissue of an tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear and complete chloroplast genome, along with annotation of encoded genes. The assembly contains 94,394 scaffolds totaling 1.17 Gb with 18,512 scaffolds of length 2 kb or longer, with a total length of 1.15 Gb and a N50 scaffold size of 278,077 kb. The k-mer histograms indicate an approximate diploid genome size of 720-730 Mb, which is smaller than the total length due to high heterozygosity, estimated at 1.25%. A comparison with a recently published European oak (Q. robur) nuclear sequence indicates 93% similarity. The Q. lobate chloroplast genome has 99% identity with another North American oak, Q. rubra Preliminary annotation yielded an estimate of 61,773 predicted protein-coding genes, of which 71% had similarity to known protein domains. We searched 956 Benchmarking Universal Single-Copy Orthologs and found 863 complete orthologs of which 450 were present in more than one copy. We also examined an earlier version (v0.5) where duplicate haplotypes were removed to discover variants. These additional sources indicate that the predicted gene count in Version1.0 is over-estimated by 37-52%. Nonetheless, this first draft valley oak genome assembly represents a high-quality, well-annotated genome that provides a tool for forest restoration and management practices.