Supporting data for "Genome sequence of agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family"

<i>Aquilaria sinensis</i> (Lour.) Spreng is one of important plant resources for producing agarwood in China. The agarwood collected from the wounded Aquilaria trees have been used for aromatic or medicinal purposes in these regions from the ancient time, whereas the mechanism underlying the formation of agarwood still remained poorly understood by a lack of accurate and high-quality genetics information. <br>We report genomic architecture of<i> A.sinensis</i> by an integrated strategy combining with Nanopore sequencing, Illumina sequencing and Hi-C sequencing. The final genome was approximately 726.5 Mb, which reached a high level of continuity with a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. Benchmarking Universal Single-Copy Orthologs evaluation reveals that the genome completeness reaches 95.27%. The repeat sequences are accounted for 59.13% and the protein-coding genes are annotated for 29,203 in the entire genome. According to phylogenetic analysis using single-copy orthologous genes, we found that <i>A.sinensis</i> is closely related to <i>Gossypium hisutum</i> and <i>Theobroma cacao</i> from the Malvales order, and <i>A.sinensis</i> was diverged from their common ancestor approximately 53.18-84.37 million years ago. <br>Here, we represent the first chromosome-level genome assembly and gene annotation of<i> A.sinensis</i>. This study would contribute to provide valuable genetic resources for the further researches on agarwood formation mechanism, genome-assisted improvements and conservation biology of Aquilaria species.