AUTHOR=Liu Dan , Xie Xiaoman , Tong Boqiang , Zhou Chengcheng , Qu Kai , Guo Haili , Zhao Zhiheng , El-Kassaby Yousry A. , Li Wei , Li Wenqing 

TITLE=A high-quality genome assembly and annotation of Quercus acutissima Carruth

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1068802

DOI=10.3389/fpls.2022.1068802

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p><italic>Quercus acutissima</italic> 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.</p></sec><sec><title>Methods</title><p>Here, we combined PacBio long reads, Hi-C, and Illumina short reads to assemble <italic>Q. acutissima</italic> genome.</p></sec><sec><title>Results</title><p>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. <italic>Ab initio</italic>, 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 <italic>Q. acutissima</italic> and <italic>Q. variabilis</italic> were differentiated around 3.6 million years ago, and showed no evidence of species-specific whole genome duplication.</p></sec><sec><title>Conclusion</title><p>The assembled and annotated high-quality <italic>Q. acutissima</italic> genome not only promises to accelerate the species molecular biology studies and breeding, but also promotes genome level evolutionary studies.</p></sec>