Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family
文献类型： 外文期刊
作者： Ding, Xupo 1 ; Mei, Wenli 1 ; Lin, Qiang 2 ; Wang, Hao 1 ; Wang, Jun 1 ; Peng, Shiqing 5 ; Li, Huiliang 5 ; Zhu, Jiahong; 1 ;
作者机构： 1.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Hainan Engn Res Ctr Agarwood, Rd Xueyuan 4, Haikou 571101, Hainan, Peoples R China
2.Guangdong Lab Lingnan Modern Agr, Shenzhen, Peoples R China
3.Minist Agr, Genome Anal Lab, Rd Pengfei 7, Shenzhen 518120, Peoples R China
4.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Rd Pengfei 7, Shenzhen 518120, Peoples R China
5.Minist Agr & Rural Affairs, Inst Trop Biosci & Biotechnol, Key Lab Biol & Genet Resources Trop Crops, Rd Xueyuan 4, Haikou 571101, Hainan, Peoples R China
6.Chinese Acad Trop Agr Sci, Rd Xueyuan 4, Haikou 571101, Hainan, Peoples R China
关键词： Aquilaria sinensis; agarwood; chromosome-level genome assembly; Hi-C sequencing; annotation
期刊名称：GIGASCIENCE （ 影响因子：6.524； 五年影响因子：8.702 ）
ISSN： 2047-217X
年卷期： 2020 年 9 卷 3 期
页码：
收录情况： SCI
摘要： Backgroud: 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. Findings: We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was similar to 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 similar to 53.18-84.37 million years ago. Conclusions: 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.
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