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Assembly and analysis of the genome of Notholithocarpus densiflorus.
Cai, Ying; Anderson, Ellis; Xue, Wen; Wong, Sylvia; Cui, Luman; Cheng, Xiaofang; Wang, Ou; Mao, Qing; Liu, Sophie Jia; Davis, John T; Magalang, Paulo R; Schmidt, Douglas; Kasuga, Takao; Garbelotto, Matteo; Drmanac, Radoje; Kua, Chai-Shian; Cannon, Charles; Maloof, Julin N; Peters, Brock A.
Affiliation
  • Cai Y; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Anderson E; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Xue W; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Wong S; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Cui L; Department of Research, BGI-Shenzhen, Shenzhen 518083, China.
  • Cheng X; Department of Research, MGI, BGI-Shenzhen, Shenzhen 518083, China.
  • Wang O; Department of Research, BGI-Shenzhen, Shenzhen 518083, China.
  • Mao Q; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Liu SJ; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Davis JT; Department of Plant Biology, University of California, Davis, CA 95616, USA.
  • Magalang PR; Department of Plant Biology, University of California, Davis, CA 95616, USA.
  • Schmidt D; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA.
  • Kasuga T; Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA 95616, USA.
  • Garbelotto M; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA.
  • Drmanac R; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
  • Kua CS; Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA.
  • Cannon C; Center for Tree Science, The Morton Arboretum, Lisle, IL 60532, USA.
  • Maloof JN; Department of Plant Biology, University of California, Davis, CA 95616, USA.
  • Peters BA; Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.
G3 (Bethesda) ; 14(5)2024 05 07.
Article in En | MEDLINE | ID: mdl-38427916
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 spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to "sudden oak death" (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread deaths of tanoaks. In this study, 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 cobarcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore long reads to 30× coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published to date, with a contig N50 of ∼1.2 Mb, a scaffold N50 of ∼2.1 Mb, and a complete gene score of 95.5% through BUSCO analysis. 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 cobarcoded data, we were able to generate a complete haplotype coverage of all 11 genomes.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Plant / Fagaceae Language: En Journal: G3 (Bethesda) Year: 2024 Type: Article Affiliation country: United States

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genome, Plant / Fagaceae Language: En Journal: G3 (Bethesda) Year: 2024 Type: Article Affiliation country: United States