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The genome draft of coconut (Cocos nucifera)

Xiao Yong, Xu Pengwei, Fan Haikuo, Baudouin Luc, Xia Wei, Bocs Stéphanie, Xu Junyang, Li Qiong, Guo Anping, Zhou Lixia, Li Jing, Wu Yi, Ma Zilong, Armero Villanueva Alix Augusto, Issali Auguste Emmanuel, Liu Na, Peng Ming, Yang Yaodong. 2017. The genome draft of coconut (Cocos nucifera). GigaScience, 6 (11), 11 p.

Journal article ; Data paper ; Article de revue à facteur d'impact Revue en libre accès total
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Url - jeu de données : http://gigadb.org/dataset/100347

Quartile : Outlier, Sujet : MULTIDISCIPLINARY SCIENCES

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. (Résumé d'auteur)

Mots-clés Agrovoc : Cocos nucifera, Génome, Phylogénie, Génétique des populations, Génie génétique, Transposition de gènes, Arabidopsis thaliana, Expression des gènes, ADN, Séquence d'ARN, Banque de gènes, technique de prévision

Mots-clés géographiques Agrovoc : Hainan

Mots-clés libres : Coconut palm, Genome, Assembly, Annotation, Arabidopsis thaliana, Maximum-likelihood, RNA-seq, Database, Sequence, Tool, Prediction, DNA, Overexpression, Transcripts

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Xiao Yong, CATAS (CHN)
  • Xu Pengwei, BGI-Shenzhen (CHN)
  • Fan Haikuo, CATAS (CHN)
  • Baudouin Luc, CIRAD-BIOS-UMR AGAP (FRA)
  • Xia Wei, CATAS (CHN)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Xu Junyang, BGI-Shenzhen (CHN)
  • Li Qiong, CATAS (CHN)
  • Guo Anping, CATAS (CHN)
  • Zhou Lixia, CATAS (CHN)
  • Li Jing, CATAS (CHN)
  • Wu Yi, CATAS (CHN)
  • Ma Zilong, CATAS (CHN)
  • Armero Villanueva Alix Augusto, CIRAD-BIOS-UMR AGAP (FRA)
  • Issali Auguste Emmanuel, CNRA (CIV)
  • Liu Na, BGI-Shenzhen (CHN)
  • Peng Ming, CATAS (CHN)
  • Yang Yaodong, CATAS (CHN)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/586851/)

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