Assembly and analysis of the genome of Notholithocarpus densiflorus

Authors: CAI, YING - Complete Genomics; ANDERSON, ELLIS - Complete Genomics; XUE, WEN - Complete Genomics; WONG, SYLVIA - Complete Genomics; CUI, LUMAN - Bgi Shenzhen; CHENG, XIAOFANG - Bgi Shenzhen; WANG, OU - Bgi Shenzhen; MAO, QING - Complete Genomics; LIU, SOPHIE - Complete Genomics; DAVIS, JOHN - University Of California, Davis; MAGALANG, PAULO - University Of California, Davis; SCHMIDT, DOUGLAS - University Of California Berkeley; Kasuga, Takao; GARBELOTTO, MATTEO - University Of California Berkeley; DRMANAC, RADOJE - Complete Genomics; KUA, CHAI-SHIAN - Morton Arboretum; CANNON, CHARLES - Morton Arboretum; MALOOF, JULIN - University Of California, Davis; PETERS, BROCK - Complete Genomics

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2024
Publication Date: 3/1/2024
Citation: Cai, Y., Anderson, E., Xue, W., Wong, S., Cui, L., Cheng, X., Wang, O., Mao, Q., Liu, S.J., Davis, J.T., Magalang, P.R., Schmidt, D., Kasuga, T., Garbelotto, M., Drmanac, R., Kua, C., Cannon, C., Maloof, J.N., Peters, B.A. 2024. Assembly and analysis of the genome of Notholithocarpus densiflorus. G3, Genes/Genomes/Genetics. 14(5). Article jkae043. https://doi.org/10.1093/g3journal/jkae043.
DOI: https://doi.org/10.1093/g3journal/jkae043

Interpretive Summary: Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. These trees are highly susceptible to ‘sudden oak death’ (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread fatality of tanoaks. Here, we sequenced the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD.

Technical Abstract: Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus), phylogenetic analysis determined that the tanoak was an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with one species. These trees are highly susceptible to ‘sudden oak death’ (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread fatality of tanoaks. Here, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using co-barcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore (ONT) long reads to 30X coverage. The draft genome reported here is one of the more contiguous and complete genomes of a tree species with a contig N50 of ~1.2 Mb and a scaffold N50 of ~2.1 Mb. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome enabling the discovery of almost 25 million single nucleotide polymorphisms and ~4.4 million small insertions and deletions. Finally, using co-barcoded data we were able to generate complete haplotype coverage of all 11 genomes.