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Data released on September 13, 2017

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

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, A, E; 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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix095

Accessions (data included in GigaDB):

BioProject: PRJNA374600

Keywords:

Coconut. Palm genome Assembly Annotation 

Genomic

http://gigadb.org/images/data/cropped/100347.jpg

Funding:

  • Funding body - Science & Technology Department of Hainan Province
  • Location - China
  • Award ID - KJHZ2014-24
  • Comment - International Science and Technology Cooperation projects of Hainan Province
  • Awardee - Y Yang
  • Funding body - Science & Technology Department of Hainan Province
  • Location - China
  • Award ID - 313058
  • Comment - Hainan Natural Science Foundation
  • Awardee - W Xia
  • Funding body - Science & Technology Department of Hainan Province
  • Location - China
  • Award ID - ZDZX2013023-1
  • Comment - Major Technology Project of Hainan
  • Awardee - M Peng
  • Funding body - Ministry of Agriculture of the People's Republic of China
  • Location - China
  • Award ID - CATAS-No.1630032012044
  • Comment - the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  • Awardee - Y Yang
  • Funding body - Ministry of Agriculture of the People's Republic of China
  • Location - China
  • Award ID - CATAS-No.1630052014002
  • Comment - the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  • Awardee - Y Yang
  • Funding body - Ministry of Agriculture of the People's Republic of China
  • Location - China
  • Award ID - CATAS-No.1630052015050
  • Comment - the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  • Awardee - Y Xiao
  • Funding body - Ministry of Agriculture of the People's Republic of China
  • Location - China
  • Award ID - CATAS-No.1630152017019
  • Comment - the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  • Awardee - Y Yang
  • Funding body - Ministry of Agriculture of the People's Republic of China
  • Location - China
  • Award ID - 17CXTD-28
  • Comment - Central Public-interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS
  • Awardee - Y Yang

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
AlignmentsUNKNOWN75.21 KB2017-08-25
AlignmentsUNKNOWN5.93 MB2017-08-25
AlignmentsUNKNOWN1.98 MB2017-08-25
annotationKEGG3.98 MB2017-08-25
annotationGFF21.54 MB2017-08-25
annotationUNKNOWN2.62 MB2017-08-25
annotationUNKNOWN2.16 MB2017-08-25
annotationUNKNOWN47.61 MB2017-08-25
annotationGFF2.1 MB2017-08-25
annotationGFF26.23 MB2017-08-25
Displaying 1-10 of 42 File(s).

History:

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