Preliminary Studies of a Genome Assembly of the California Endemic Oak, Quercus lobata Née (Fagaceae) using Pacific Biosciences and Illumina Sequencing Data

Oaks represent a valuable natural resource across the Northern Hemisphere with a large research community studying their genetics, systematics, ecology, conservation, and management. We report our progress on assembling the genome sequence of valley oak (Quercus lobata) using both Pacific Biosciences (PacBio) and Illumina sequencing data from adult leaf tissue of an individual found in a natural population. We compare three assemblies: Illumina only, PacBio only, and a hybrid combining both data sets. The Illumina assembly, performed with MaSuRCA and SOAPdenovo2, consists 18,512 scaffolds of length >2 kb totaling 1.15 Gb, with N50 scaffold size of 278 kb. The k-mer histograms indicate an approximate diploid genome size of 700-740 Mb, which is smaller than the assembled length due to the high heterozygosity in this outcrossing tree species. The PacBio assembly, performed with Canu, consists of 7,300 assembled contigs totaling 0.97 Gb with N50 of 429 kb, plus unassembled sequences totaling 3.31 Gb. The hybrid assembly was performed with the MaSuRCA Assembler using error-corrected PacBio reads, yielding a draft nuclear genome of 25,683 unitigs totaling 1.31 Gb with N50 size of 880 kb. We are working on methods to decrease the haplotype redundancy to yield a final genome assembly closer to the expected 730 Mb. We will also build on our previous Maker annotation models to complete a comprehensive carefully curated structural and functional annotation for our final genome. This high-quality, well-annotated genome will allow researchers to identify the molecular basis of traits important to the sustainability and management of oaks.