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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)3485-3495
Number of pages11
JournalG3: Genes, Genomes, Genetics
Volume6
Issue number11
DOIs
StatePublished - 2016

Keywords

  • Adaptation
  • Annotation
  • Chloroplast
  • GenPred
  • Genomic Selection
  • Nuclear genome assembly
  • Quercus
  • Shared Data Resources

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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  • Cite this

    Sork, V. L., Fitz-Gibbon, S. T., Puiu, D., Crepeau, M., Gugger, P. F., Sherman, R., Stevens, K., Langley, C. H., Pellegrini, M., & Salzberg, S. L. (2016). First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae). G3: Genes, Genomes, Genetics, 6(11), 3485-3495. https://doi.org/10.1534/g3.116.030411