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

Dataset type: Genomic
Data released on January 21, 2020

Ding X; Mei W; Lin Q; Wang H; Wang J; Peng S; Li H; Zhu J; Li W; Wang P; Chen H; Dong W; Guo D; Cai C; Huang S; Cui P; Dai H (2020): Supporting data for "Genome sequence of agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family" GigaScience Database. http://dx.doi.org/10.5524/100702

DOI10.5524/100702

Aquilaria sinensis (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.
We report genomic architecture of A.sinensis 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 A.sinensis is closely related to Gossypium hisutum and Theobroma cacao from the Malvales order, and A.sinensis was diverged from their common ancestor approximately 53.18-84.37 million years ago.
Here, we represent the first chromosome-level genome assembly and gene annotation of A.sinensis. 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.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 32118265)

Accessions (data generated as part of this study):

BioProject: PRJNA556948





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN12385133210372  Aquilaria sinensis Description:DNA extracted from mature leaves of ag...
Alternative accession-BioProject:PRJNA556948
Common name:Agarwood; Eaglewood; Baimuxiang
...
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SAMN13867374210372  Aquilaria sinensis Description:RNA extracted from mixed mature leaves...
Alternative accession-BioProject:PRJNA556948
Common name:Agarwood; Eaglewood; Baimuxiang
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherTEXT0.75 KB2020-01-17
AnnotationFASTA32.59 MB2020-01-17
Sequence assemblyFASTA692.93 MB2020-01-17
AnnotationGFF11.65 MB2020-01-17
AlignmentsTAR72.75 MB2020-01-17
AnnotationGFF285.26 KB2020-01-17
Protein sequenceFASTA12.25 MB2020-01-17
Phylogenetic treeUNKNOWN0.51 KB2020-01-17
ReadmeTEXT3.5 KB2020-01-21
AnnotationGFF184.98 MB2020-01-17
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences W Mei 17CXTD-15
National Natural Science Foundation of China W Mei 31870668
Earmarked Fund for China Agriculture Research System H Dai CARS-21
Date Action
January 21, 2020 Dataset publish
March 16, 2020 Manuscript Link added : 10.1093/gigascience/giaa013
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giaa013