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

Victoria L Sork; Sorel T Fitz-Gibbon; Daniela Puiu; Marc Crepeau; Paul F Gugger; Rachel Sherman; Kristian Stevens; Charles H Langley; Matteo Pellegrini; Steven L Salzberg

doi:10.1534/g3.116.030411

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

G3 (Bethesda). 2016 Nov 8;6(11):3485-3495. doi: 10.1534/g3.116.030411.

Authors

Victoria L Sork^{1

2}, Sorel T Fitz-Gibbon³, Daniela Puiu⁴, Marc Crepeau⁵, Paul F Gugger^{6

7}, Rachel Sherman^{8

9}, Kristian Stevens⁵, Charles H Langley⁵, Matteo Pellegrini⁹, Steven L Salzberg^{8

9

10

11}

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095 vlsork@ucla.edu.
² Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095.
³ Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095.
⁴ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
⁵ Department of Evolution and Ecology, University of California, Davis, California 95616.
⁶ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095.
⁷ University of Maryland Center for Environmental Science, Appalachian Laboratory, Frostburg, Maryland 21532.
⁸ Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218.
⁹ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095.
¹⁰ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.
¹¹ Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21218.

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.

Keywords: GenPred; Genomic Selection; Quercus; Shared Data Resources; adaptation; annotation; chloroplast; nuclear genome assembly.

Grants and funding

R01 HG006677/HG/NHGRI NIH HHS/United States