A high-quality genome assembly and annotation of Quercus acutissima Carruth
Dan Liu, Xiaoman Xie, Boqiang Tong, Chengcheng Zhou, Kai Qu, Haili Guo, Zhiheng Zhao, Yousry A. El‐Kassaby, Wei Li, Wenqing Li
Abstract
Introduction Quercus acutissima is an economic and ecological tree species often used for afforestation of arid and semi-arid lands and is considered as an excellent tree for soil and water conservation. Methods Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble Q. acutissima genome. Results We generated a 957.1 Mb genome with a contig N50 of 1.2 Mb and scaffold N50 of 77.0 Mb. The repetitive sequences constituted 55.63% of the genome, among which long terminal repeats were the majority and accounted for 23.07% of the genome. Ab initio , homology-based and RNA sequence-based gene prediction identified 29,889 protein-coding genes, of which 82.6% could be functionally annotated. Phylogenetic analysis showed that Q. acutissima and Q. variabilis were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication. Conclusion The assembled and annotated high-quality Q. acutissima genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.