Chromosome-level genome assembly of Daemonorops jenkinsiana

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 Daemonorops jenkinsiana GigaScience Database. http://dx.doi.org/10.5524/101053

DOI10.5524/101053

Daemonorops jenkinsiana is a rattan palm in the family Arecaceae, found primarily in the tropics and subtropics of southeastern Asia including southern China. It is one of the most significant material sources for the rattan industry with their stems being harvested for their cores, which is used for everything from canes to furniture.
The lack of any reference genome sequences is a major obstacle for basic and applied biology of rattan. Here we provide the chromosome-level genome assembly of D. jenkinsiana using the Illumina, PacBio, and Hi-C sequencing data. A total of ~682 Gb of raw data covering the predicted genome length of ~1.61 Gb with ~ 426× read depth.
The de novo genome assembly of ~1.58 Gb was generated with scaffold N50 of ~119 Mb and 53,342 intact predicted protein-coding gene models. BUSCO evaluation demonstrated a genome completeness of 91.3%.
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

Read the peer-reviewed publication(s):


Related datasets:

doi:10.5524/101053 IsSupplementTo doi:10.5524/100480

Accessions (data generated as part of this study):

BioProject: PRJEB24829

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Djen-XB-1-1A1510057  Daemonorops jenkinsiana Description:DNA was extracted from young leaves at...
Alternative accession-BioSample:SAMEA104569509
Geographic location (latitude and longitude):23.19...
...
+
Djen-XB-1-2A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-1-3A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-1-4A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-2-1A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-2-2A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-2-3A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-2-4A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-3-1A1510057  Daemonorops jenkinsiana Description:RNA was extracted from the distal cirr...
Geographic location (latitude and longitude):23.19...
Geographic location (country and/or sea,region):Gu...
...
+
Djen-XB-3-2A1510057  Daemonorops jenkinsiana 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 
annotationGFF74.73 MB2018-07-09
Coding SequenceFASTA58.15 MB2018-07-09
annotationGFF18.21 MB2018-07-09
protein sequenceFASTA20.71 MB2018-07-09
Genome sequenceFASTA444.48 MB2018-07-09
annotationGFF25.67 KB2018-07-09
annotationGFF113.13 KB2018-07-09
annotationGFF300.61 KB2018-07-09
annotationGFF84.32 KB2018-07-09
Genome sequenceFASTA434.68 MB2018-07-09
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
February 6, 2019 Relationship removed : DOI 100504
February 6, 2019 Manuscript Link added : 10.1093/gigascience/giy097