A chromosome-scale genome assembly of Quercus gilva: Insights into the evolution of Quercus section Cyclobalanopsis (Fagaceae)

<em>Quercus gilva</em> is an ecologically and economically important species of <em>Quercus</em> section <em>Cyclobalanopsis</em> and is a dominant species in evergreen broad-leaved forests in subtropical regions of East Asia. In the present study, we reported a high-quality chromosome-scale genome assembly of <em>Q. gilva</em>, the first reference genome for section <em>Cyclobalanopsis</em>, using the combination of Illumina and PacBio sequencing with Hi-C technologies. The assembled genome size of <em>Q. gilva</em> was 889.71 Mb, with a contig number of 773 and a contig N50 of 28.32 Mb. Hi-C scaffolding anchored 859.07 Mb contigs (96.54% of the assembled genome) onto 12 pseudochromosomes, with a scaffold N50 of 70.35 Mb. A combination of de novo, homology-based, and transcript-based predictions predicted a final set of 36,442 protein-coding genes distributed on 12 pseudochromosomes, and 97.73% of them were functionally annotated. A total of 535.64 Mb (60.20%) of repetitive sequences were identified. Genome evolution analysis revealed that <em>Q. gilva</em> was most closely related to <em>Q. suber</em> and they diverged at 40.35 Ma, and <em>Q. gilva</em> did not experience species-specific whole-genome duplication in addition to the ancient <em>gamma</em> whole-genome triplication event shared by core eudicot plants. <em>Q. gilva</em> underwent considerable gene family expansion and contraction, with 598 expanded and 6,509 contracted gene families detected. The first chromosome-scale genome of<em> Q. gilva</em> will promote its germplasm conservation and genetic improvement and provide essential resources for better studying the evolution of <em>Quercus </em>section <em>Cyclobalanopsis</em>.