Valley Oak Genome Sequence 1.0

1. Assembly and preliminary annotation of nuclear and chloroplast DNA sequences derived from a California endemic oak, Quercus lobata Née (Fagaceae)
Participants: Victoria Sork, Steven Salzberg, Matteo Pellegrini, Paul Gugger, Jessica Wright, Chuck Langley, Sorel Fitz-Gibbon, Daniela Puiu, Shawn Cokus, Lawren Sack, Marc Crepeau, Kristin Stevens, Geo Pertea, Rachel Sherman

Authors: Victoria L. Sork, Sorel T. Fitz-Gibbon, Daniela Puiu, Marc Crepeau, Paul F. Gugger, Rachel Sherman, Kristian Stevens, Charles H. Langley, Matteo Pellegrini and Steven Salzberg
Abstract
Oak represents 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 lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a 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 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. lobata 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 > 1 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 Version 1.0 is overestimated 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

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Data links for this study:

–  Valley Oak Genome 1.0 FASTA file.  Download
–  Valley Oak Genome 0.5 (reduced) FASTA file. Download
–  Valley Oak Genome 0.5 annotation gff file, Download
–  UCSC Genome Browser for Quercus lobata