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

Quercus oxyphylla (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 Q. oxyphylla 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 Q. oxyphylla 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 Quercus and indicated that Q. oxyphylla possibly split with the ancestor of Cerris oaks about 20.4 million years ago. We identified 2074 expanded and 903 contracted gene families across the genome assembly of Q. oxyphylla, 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 Q. oxyphylla generated in this study provides a valuable genome resource for the genetic conservation and management of Q. oxyphylla, and may facilitate our understanding of genome evolution and species adaptation of the oak lineage.