Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Rd. Xueyuan No. 4, Haikou 571101, China.
Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Rd. Pengfei No. 7, Shenzhen 518120, China.
Gigascience. 2020 Mar 1;9(3). doi: 10.1093/gigascience/giaa013.
Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information.
We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and 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. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18-84.37 million years ago.
Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.
白木香（Aquilaria sinensis（Lour.）Spreng）是中国沉香生产的重要植物资源之一。从古至今，从受伤的沉香树上采集的沉香树脂一直被亚洲人用于芳香或药用目的，尽管由于缺乏准确和高质量的遗传信息，沉香的形成机制仍知之甚少。
我们通过结合纳米孔、Illumina 和 Hi-C 测序的综合策略报告了白木香的基因组结构。最终基因组大小约为 726.5Mb，达到了较高的连续性，并且连续体 N50 为 1.1Mb。我们将 Hi-C 数据与基因组组装相结合，生成了染色体水平的支架。将 8 个超级支架与 8 条染色体相对应，组装成最终大小为 716.6Mb 的染色体，使用 1862 个连续体，支架 N50 为 88.78Mb。BUSCO 评估表明基因组完整性达到 95.27%。重复序列占 59.13%，基因组中注释了 29203 个蛋白质编码基因。根据使用单拷贝直系同源基因进行的系统发育分析，我们发现白木香与锦葵目（Malvales order）的陆地棉（Gossypium hirsutum）和可可（Theobroma cacao）关系密切，白木香与它们的共同祖先分化的时间约为 53.18-84.37 百万年前。
本研究提供了白木香的首个染色体水平基因组组装和基因注释。这项研究应该为进一步研究沉香形成机制、基于基因组的改良以及沉香属物种的保护生物学提供有价值的遗传资源。
