The genome draft of coconut (Cocos nucifera).

التفاصيل البيبلوغرافية
العنوان:	The genome draft of coconut (Cocos nucifera).
المؤلفون:	Xiao Y; 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., Xu P; BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China., Fan H; 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., Baudouin L; AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.; CIRAD, UMR AGAP, F-34398, Montpellier France., Xia W; 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., Bocs S; AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.; CIRAD, UMR AGAP, F-34398, Montpellier France., Xu J; BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China., Li Q; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China., Guo A; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China., Zhou L; 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., Li J; 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., Wu Y; 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., Ma Z; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China., Armero A; AGAP, Université de Montpellier, CIRAD, INRA, Montpellier Supagro, F-34398, Montpellier, France.; Montpellier Supagro, UMR AGAP, F-34398, Montpellier, France., Issali AE; Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA) 07 B.P. 13, Port Bouet, Côte d'Ivoire., Liu N; BGI Genomics, BGI-Shenzhen, Building NO.7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China., Peng M; Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Rd. Xueyuan No. 4, Haikou, Hainan 571101, P. R. China., Yang Y; 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.
المصدر:	GigaScience [Gigascience] 2017 Nov 01; Vol. 6 (11), pp. 1-11.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't
اللغة:	English
بيانات الدورية:	Publisher: Oxford University Press Country of Publication: United States NLM ID: 101596872 Publication Model: Print Cited Medium: Internet ISSN: 2047-217X (Electronic) Linking ISSN: 2047217X NLM ISO Abbreviation: Gigascience Subsets: MEDLINE
أسماء مطبوعة:	Publication: 2017- : New York : Oxford University Press Original Publication: London : BioMed Central
مواضيع طبية MeSH:	Genome, Plant* , Molecular Sequence Annotation, Cocos/genetics
مستخلص:	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. (© The Author 2017. Published by Oxford University Press.)
References:	Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4. (PMID: 17151080) Nat Biotechnol. 2010 May;28(5):511-5. (PMID: 20436464) Nature. 2009 Jan 29;457(7229):551-6. (PMID: 19189423) Nat Commun. 2013;4:2274. (PMID: 23917264) Genome Res. 2004 May;14(5):988-95. (PMID: 15123596) Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717) Molecules. 2009 Dec 09;14(12):5144-64. (PMID: 20032881) J Exp Bot. 2007;58(2):301-8. (PMID: 17229760) Nucleic Acids Res. 2000 Jan 1;28(1):231-4. (PMID: 10592234) Nucleic Acids Res. 2000 Jan 1;28(1):263-6. (PMID: 10592242) Nucleic Acids Res. 1999 Jan 1;27(1):29-34. (PMID: 9847135) J Mol Biol. 1997 Apr 25;268(1):78-94. (PMID: 9149143) Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6. (PMID: 19036790) Gigascience. 2017 Nov 1;6(11):1-11. (PMID: 29048487) Nature. 2000 Dec 14;408(6814):796-815. (PMID: 11130711) Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9. (PMID: 16845043) Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10. (PMID: 19274634) Gigascience. 2012 Dec 27;1(1):18. (PMID: 23587118) Science. 2009 Nov 20;326(5956):1112-5. (PMID: 19965430) Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189. (PMID: 27899595) Nat Biotechnol. 2003 Jan;21(1):81-5. (PMID: 12469134) Bioinformatics. 2014 May 1;30(9):1236-40. (PMID: 24451626) Cytogenet Genome Res. 2005;110(1-4):462-7. (PMID: 16093699) Science. 2002 Apr 5;296(5565):92-100. (PMID: 11935018) Nucleic Acids Res. 2000 Jan 1;28(1):225-7. (PMID: 10592232) Mol Biol Evol. 2007 Aug;24(8):1586-91. (PMID: 17483113) PLoS One. 2013;8(3):e59997. (PMID: 23555859) Nucleic Acids Res. 1999 Jan 15;27(2):573-80. (PMID: 9862982) Nucleic Acids Res. 2000 Jan 1;28(1):45-8. (PMID: 10592178) Bioinformatics. 2009 May 1;25(9):1105-11. (PMID: 19289445) Genome Res. 2003 Sep;13(9):2178-89. (PMID: 12952885) Genome Res. 2002 Apr;12(4):656-64. (PMID: 11932250) Science. 2006 Sep 15;313(5793):1596-604. (PMID: 16973872) Database (Oxford). 2012 Feb 01;2012:bar068. (PMID: 22301074) Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. (PMID: 9254694) Nucleic Acids Res. 1999 Jan 1;27(1):263-7. (PMID: 9847197) Nature. 2013 Aug 15;500(7462):335-9. (PMID: 23883927) Nat Biotechnol. 2011 May 29;29(6):521-7. (PMID: 21623354) Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8. (PMID: 17485477) Nucleic Acids Res. 1980 Oct 10;8(19):4321-5. (PMID: 7433111) Genome Biol. 2007;8(1):R13. (PMID: 17241472) Bioinformatics. 2004 Nov 1;20(16):2878-9. (PMID: 15145805) Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. (PMID: 15034147) Syst Biol. 2010 May;59(3):307-21. (PMID: 20525638)
فهرسة مساهمة:	Keywords: annotation; assembly; coconut palm; genome
تواريخ الأحداث:	Date Created: 20171020 Date Completed: 20180709 Latest Revision: 20220331
رمز التحديث:	20221213
مُعرف محوري في PubMed:	PMC5714197
DOI:	10.1093/gigascience/gix095
PMID:	29048487
قاعدة البيانات:	MEDLINE

Full Text Finder

الوصف
تدمد:	2047-217X
DOI:	10.1093/gigascience/gix095