Chromosome-level genome assembly of Calamus simplicifolius

Dataset type: Genomic, Transcriptomic
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): Chromosome-level genome assembly of Calamus simplicifolius GigaScience Database. http://dx.doi.org/10.5524/101052

DOI10.5524/101052

Calamus simplicifolius is a spiny, evergreen, climbing palm, usually forming an open cluster of vigorous, unbranched stems that can reach a length of 50 metres and about 12 - 15mm in diameter. This species produces cane of medium diameter, supreme for all types of binding and weaving in the furniture industry and widely used in China for cordage, house construction and the finest basketware.
The lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Here we provide the chromosome-level genome assembly of C. simplicifolius using the Illumina, PacBio, and Hi-C sequencing data. A total of ~730 Gb of raw data covering the predicted genome length ~1.98 Gb to ~ 372× read depth. The de novo genome assembly of ~1.94 Gb generated a scaffold N50 of ~160 Mb with 51,235 intact predicted protein-coding gene models. BUSCO evaluation demonstrated that the genome completeness reached 96.4%.
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 a reference genome for performing comparative studies between and among different species.

Additional details

Related datasets:

doi:10.5524/101052 IsSupplementTo doi:10.5524/100480

Accessions (data included in GigaDB):

BioProject: PRJEB24031
BioProject: PRJEB24828

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Csim-XB-1-1A746888  Calamus simplicifolius Description:DNA was extracted from young leaves at...
Alternative accession-BioSample:SAMEA104569509
Geographic location (latitude and longitude):23.19...
...
+
Csim-XB-1-2A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-1-3A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-1-4A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-2-1A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-2-2A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-2-3A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-2-4A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-3-1A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Csim-XB-3-2A746888  Calamus simplicifolius Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Displaying 1-10 of 12 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Coding SequenceFASTA53.98 MB2018-07-09
annotationGFF21.38 MB2018-07-09
protein sequenceFASTA20.96 MB2018-07-09
file_typeFASTA539.46 MB2018-07-09
annotationGFF23.75 KB2018-07-09
annotationGFF200.09 KB2018-07-09
annotationGFF405.24 KB2018-07-09
annotationGFF101.7 KB2018-07-09
file_typeFASTA531.02 MB2018-07-09
Coding SequenceFASTA16.85 KB2018-07-09
Displaying 1-10 of 47 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