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Apr, 2024;24 (3): e13914.

High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics.

Chang-Sha Luo, Tian-Tian Li, Xiao-Long Jiang, Ying Song, Ting-Ting Fan, Xiang-Bao Shen, Rong Yi, Xiao-Ping Ao, Gang-Biao Xu, Min Deng
Author Information
  1. Chang-Sha Luo: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  2. Tian-Tian Li: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  3. Xiao-Long Jiang: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China. ORCID
  4. Ying Song: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  5. Ting-Ting Fan: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  6. Xiang-Bao Shen: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  7. Rong Yi: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  8. Xiao-Ping Ao: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  9. Gang-Biao Xu: The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, Hunan, China.
  10. Min Deng: School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China.
PMID: 38108568 DOI: 10.1111/1755-0998.13914

Abstract

Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high-quality haplotype-resolved reference genome was assembled for Q. glauca from PacBio HiFi and Hi-C reads. The genome size, contig N50, and scaffold N50 measured 902.88, 7.60, and 69.28 Mb, respectively, for haplotype1, and 913.28, 7.20, and 71.53 Mb, respectively, for haplotype2. A total of 37,457 and 38,311 protein-coding genes were predicted in haplotype1 and haplotype2, respectively. Homologous chromosomes in the Q. glauca genome had excellent gene pair collinearity. The number of R-genes in Q. glauca was similar to most East Asian oaks but less than oak species from Europe and America. Abundant structural variation in the Q. glauca genome could contribute to environmental stress tolerance in Q. glauca. Sections Cyclobalanopsis and Cerris diverged in the Oligocene, in agreement with fossil records for section Cyclobalanopsis, which document its presence in East Asia since the early Miocene. The demographic dynamics of closely related oak species were largely similar. The high-quality reference genome provided here for the most widespread species in section Cyclobalanopsis will serve as an essential genomic resource for evolutionary studies of key oak lineages while also supporting studies of interspecific introgression, local adaptation, and speciation in oaks.

Keywords

Fagaceae PSMC’ east Asian evergreen broadleaved forests evolution

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Grants

  1. CX20210882/Hunan Provincial Innovation Foundation for Postgraduate
  2. 31700174/National Natural Science Foundation of China
  3. 31972858/National Natural Science Foundation of China
  4. 2022JJ40861/Natural Science Foundation of Hunan Province
  5. 21A0158/Research Fund of Hunan Provincial Education Department

MeSH Term

Quercus
Phylogeny
Haplotypes
Forests
Demography
Journal Article

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