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

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.

The complete chloroplast genome sequence of Quercus schottkyana, and comparative analysis with related species.

In this study, we sequenced the complete chloroplast genome of Quercus schottkyana. The circular genome is 160,746 bp in size, featuring a typical quadripartite structure comprising one large single-copy region (LSC, 90,136 bp), one small single-copy region (SSC, 18,942 bp), and two copies of inverted repeat regions (IRs, 25,834 bp). The genome contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content is 36.90%. The maximum likelihood phylogenetic tree reconstructed using IQ-TREE indicated that Q. schottkyana has a closer relationship with Quercus sichourensis and Quercus acuta.

The complete chloroplast genome sequence of Quercus chungii (Fagaceae).

Quercus chungii F.P.Metcalf, a rare oak with endemic to southern China, belongs to the compound trichome base (CTB) lineage in the Cyclobalanopsis section. The complete chloroplast genome of the species was assembled and annotated in this study. The circular genome was 160,731 bp in size, presenting a typical quadripartite structure including one large single-copy region (LSC, 90,140 bp), one small single-copy region (SSC, 18,911 bp), and two copies of inverted repeat regions (IRs, 25,840 bp). It encoded a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The maximum-likelihood (ML) phylogenetic tree reconstructed by IQ-TREE indicated that Q. chungii was more closely related to Q. myrsinifolia and Q. sichourensis.