Supporting data for "The genome draft of Coconut (Cocos nucifera)"

Dataset type: Genomic
Data released on September 13, 2017

Xiao Y; Xu P; Fan H; Baudouin L; Xia W; Bocs S; Xu J; Li Q; Guo A; Zhou L; Li J; Wu Y; Ma Z; Armero A; Issali AE; Liu N; Peng M; Yang Y (2017): Supporting data for "The genome draft of Coconut (Cocos nucifera)" GigaScience Database. http://dx.doi.org/10.5524/100347

DOI10.5524/100347

Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific island, with a total growth area of more than 12 million hectares (www.fao.org/faostat/en/). Coconut palm is generally classified into two main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of Cocos nucifera genome: a major genomic resource which could be used to facilitate molecular breeding in Cocos nucifera and accelerating the breeding process in this important crop.
A total of 419.67 gigabases (Gb) of raw reads were generated by the IlluminaHiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42Gb, variety "Hainan Tall") to an estimated 173.32× read depth. A total scaffold length of 2.20 Gb was generated (N50 =418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28,039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30 variety: 28,889), Phoenix dactylifera (DPV01 variety: 41,660) and Elaeis guineensis (34,802). BUSCO evaluation demonstrated the obtained scaffold sequences covered 90.8% of the coconut genome, and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome was consisted of transposable elements. of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may occurred in coconut involving Na+/H+ antiporter, Carnitine/acylcarnitine translocase, Potassium-dependent sodium-calcium exchanger, and potassium channel genes.

Additional details

Read the peer-reviewed publication(s):

Xiao, Y., Xu, P., Fan, H., Baudouin, L., Xia, W., Bocs, S., … Yang, Y. (2017). The genome draft of coconut (Cocos nucifera). GigaScience, 6(11), 1–11. doi:10.1093/gigascience/gix095

Accessions (data included in GigaDB):

BioProject: PRJNA374600





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Coconut sample13894 coconut palmCocos nucifera Description:mix sample from coconut leave and frui...
Analyte type:RNA
Alternative accession-BioSample:SAMN01774116
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Hainan Tall coconut13894 coconut palmCocos nucifera Description:tropical oil and friut crop
Analyte type:DNA
Alternative accession-BioSample:SAMN06328965
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
annotationUNKNOWN4.1 MB2017-08-25
annotationUNKNOWN5.25 MB2017-08-25
annotationGFF44.6 MB2017-08-25
transcriptome sequenceFASTA11.19 MB2017-08-25
Phylogenetic treeUNKNOWN0.84 KB2017-08-25
imageUNKNOWN10.97 KB2017-08-25
AlignmentsUNKNOWN5.93 MB2017-08-25
AlignmentsUNKNOWN75.21 KB2017-08-25
AlignmentsUNKNOWN1.98 MB2017-08-25
SoftwareTAR21.2 MB2017-08-25
Displaying 31-40 of 42 File(s).
Funding body Awardee Award ID Comments
Science & Technology Department of Hainan Province Y Yang KJHZ2014-24 International Science and Technology Cooperation projects of Hainan Province
Science & Technology Department of Hainan Province W Xia 313058 Hainan Natural Science Foundation
Science & Technology Department of Hainan Province M Peng ZDZX2013023-1 Major Technology Project of Hainan
Ministry of Agriculture of the People's Republic of China Y Yang CATAS-No.1630032012044 the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
Ministry of Agriculture of the People's Republic of China Y Yang CATAS-No.1630052014002 the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
Ministry of Agriculture of the People's Republic of China Y Xiao CATAS-No.1630052015050 the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
Ministry of Agriculture of the People's Republic of China Y Yang CATAS-No.1630152017019 the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
Ministry of Agriculture of the People's Republic of China Y Yang 17CXTD-28 Central Public-interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS
Date Action
September 13, 2017 Dataset publish
October 17, 2017 Manuscript Link added : 10.1093/gigascience/gix095