Chromosome-Level Genome Assembly and Comparative Genomic Analysis of <i>Quercus oxyphylla</i>, an Evergreen Subalpine Oak Species Endemic to China

<i>Quercus oxyphylla</i> (E. H. Wilson) Hand.-Mazz. is a threatened evergreen subalpine tree species with fragmented habitats native to China. Here, we present a de novo chromosome-level genome assembly of this oak species by integrating PacBio long-read high-fidelity (HiFi) sequencing and Hi-C mapping technologies. The assembled genome size of <i>Q. oxyphylla</i> in this study is 824.15 megabases (Mb) in length with 12 putative chromosomes. Genome annotation of this oak species identified 514.09 Mb of repeat sequences, 53,730 protein-coding genes and 1048 non-coding RNA sequences. Genomic analyses of whole-genome duplication (WGD) and long terminal repeat retrotransposon (LTR-RT) insertion events in <i>Q. oxyphylla</i> revealed no species-specific WGD and recent accumulation of LTR-RTs in the genome within the last seven million years. A phylogenomic analysis with eight oak representatives confirmed the framework phylogeny of genus <i>Quercus</i> and indicated that <i>Q. oxyphylla</i> possibly split with the ancestor of <i>Cerris</i> oaks about 20.4 million years ago. We identified 2074 expanded and 903 contracted gene families across the genome assembly of <i>Q. oxyphylla</i>, while the significantly expanded gene families had notable disease resistance-related genes that were mainly enriched in plant-pathogen interaction pathways. The high-quality genome assembly of <i>Q. oxyphylla</i> generated in this study provides a valuable genome resource for the genetic conservation and management of <i>Q. oxyphylla</i>, and may facilitate our understanding of genome evolution and species adaptation of the oak lineage.