Supporting data for "The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)"

Dataset type: Genomic
Data released on July 18, 2018

Zhao H; Wang S; Wang J; Chen C; Hao S; Chen L; Fei B; Han K; Li R; Shi C; Sun H; Wang S; Xu H; Yang K; Xu X; Shan X; Shi J; Feng A; Fan G; Liu X; Zhao S; Zhang C; Gao Q; Gao Z; Jiang Z (2018): Supporting data for "The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)" GigaScience Database. http://dx.doi.org/10.5524/100480

DOI10.5524/100480

Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, as the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan.
We rendered the two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using the Illumina, PacBio, and Hi-C sequencing data. A total of ~730 Gb and ~682 Gb of raw data covered the predicted genome length (~1.98 Gb of C. simplicifolius and ~1.61 Gb of D. jenkinsiana) to ~ 372× and ~ 426× read depth, respectively. The two de novo genome assemblies of ~1.94 Gb and ~1.58 Gb are generated with the scaffold N50 of ~160 Mb and ~119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genome were predicted to harbor 51,235 and 53,342 intact protein-coding gene models, respectively. BUSCO evaluation demonstrated that the genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genome, respectively. Genome evolution showed that four Arecaceae plants were located in a cluster and the divergence time between the two rattans was ~19.3 Mya. Additionally, we genome-widely identified 193 and 172 genes involved in the lignin biosynthesis pathway in C. simplicifolius and D. jenkinsiana, respectively.
We present the first de novo assemblies of the two rattan genomes (C. simplicifolius and D. jenkinsiana). These essential data will not only provide a fundamental resource of functional genomics particularly in promoting germplasm utilization for breeding improved rattan material property, but also will serve as two reference genomes for performing comparative studies between and among different species.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 30101322)

Related datasets:

doi:10.5524/100480 IsSupplementedBy doi:10.5524/101052
doi:10.5524/100480 IsSupplementedBy doi:10.5524/101053

Accessions (data generated as part of this study):

BioProject: PRJEB24031
BioProject: PRJEB24828

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Csim-Rattan746888  Calamus simplicifolius Description:DNA was extracted from the leaf at the...
Geographic location (country and/or sea,region):Gu...
Tissue:Leaf
...
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Djen-Rattan1510057  Daemonorops jenkinsiana Description:DNA was extracted from the leaf at the...
Geographic location (country and/or sea,region):Gu...
Tissue:Leaf
...
+
Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsTEXT3.65 MB2018-07-09
ScriptUNKNOWN5.53 KB2018-07-09
ScriptUNKNOWN5.45 KB2018-07-09
ImageJPG1.67 MB2018-07-09
ImageJPG4.84 MB2018-07-09
ImageJPG1.14 MB2018-07-09
ImageJPG604.97 KB2018-07-09
ImageJPG866.07 KB2018-07-09
ImageJPG2.78 MB2018-07-09
ImageJPG844.35 KB2018-07-09
Displaying 1-10 of 26 File(s).
Funding body Awardee Award ID Comments
MOST H Zhao 2015BAD04B03 Sub-Project of the National Science and Technology Support Plan of the Twelfth Five-Year Plan in China

Protocols.io:

Date Action
July 18, 2018 Dataset publish
August 22, 2018 Manuscript Link added : 10.1093/gigascience/giy097
November 11, 2022 Manuscript Link updated : 10.1093/gigascience/giy097
November 15, 2022 Data type for File lignin-genes.tar.gz updated
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.rf7d3rn
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.rf4d3qw
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.rf3d3qn