A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Abstract

<i>Quercus variabilis</i> (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from <i>Q. variabilis</i> are still lacking. Here, we present a high-quality <i>Q. variabilis</i> genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used <i>ab initio</i>, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that <i>Q. variabilis</i> was more closely related to <i>Q. suber</i> than to <i>Q. lobata</i> or <i>Q. robur.</i> We found no evidence for species-specific whole genome duplications in <i>Quercus</i> after the species had diverged. This study provides the first genome assembly and the first gene annotation data for <i>Q. variabilis.</i> These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.