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11 01, 2017;6 (11): 1-11.

The genome draft of coconut (Cocos nucifera).

Yong Xiao, Pengwei Xu, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Junyang Xu, Qiong Li, Anping Guo, Lixia Zhou, Jing Li, Yi Wu, Zilong Ma, Alix Armero, Auguste Emmanuel Issali, Na Liu, Ming Peng, Yaodong Yang
Author Information
  1. Yong Xiao: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  2. Pengwei Xu: BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.
  3. Haikuo Fan: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  4. Luc Baudouin: AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.
  5. Wei Xia: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  6. Stéphanie Bocs: AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.
  7. Junyang Xu: BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.
  8. Qiong Li: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China.
  9. Anping Guo: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China.
  10. Lixia Zhou: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  11. Jing Li: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  12. Yi Wu: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
  13. Zilong Ma: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China.
  14. Alix Armero: AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.
  15. Auguste Emmanuel Issali: Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA) 07 B.P. 13, Port Bouet, Côte d'Ivoire.
  16. Na Liu: BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.
  17. Ming Peng: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China.
  18. Yaodong Yang: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Av. Wenqing No. 496, Wenchang, Hainan 571339, P. R. China.
PMID: 29048487 DOI: 10.1093/gigascience/gix095

Abstract

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 Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 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 the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, 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: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that 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 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 have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.

Keywords

annotation assembly coconut palm genome

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MeSH Term

Cocos
Genome, Plant
Molecular Sequence Annotation
Journal Article Research Support, Non-U.S. Gov't

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