10/11/2017
With the
joint efforts of Coconut Research Institute, Chinese
Academy of Tropical Agricultural Sciences (CRI-CATAS),
Institute of Tropical
Bioscience and Biotechnology, Chinese Academy of Tropical
Agricultural Science
(ITBB-CATAS), BGI-Shenzhen, AGAP, Université de
Montpellier, CIRAD, INRA,
Montpellier Supagro and Station Cocotier Marc Delorme,
Centre National De
RechercheAgronomique (CNRA) 07 B.P. 13, Port Bouet,Côte
d'Ivoire, we have
finished the coconut whole genome sequencing of Hainan Tall
coconut. The genome
draft of coconut (Cocos nucifer) paper has been
published online on
GigaScience. The following is the link
https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/gix095/4345653/The-genome-draft-of-coconut-Cocos-nucifera?guestAccessKey=61ab3690-1962-46df-86ff-0c1f60a3e5a2
The genome draft of coconut (Cocos
nucifera)
Abstract
Background
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.
Findings
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
(2.42Gb, 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.
Conclusions
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.
--------------------------------------------------------
Yaodong Yang，
PhD
Coconut Research
Institute(CRI)/Tropical Oil Crops Research
Institute(TOCRI)
Chinese Academy
of Tropical Agricultural Sciences(CATAS)
Wenchang,
Hainan, 571339,
China.
Tel:0086-898-63330602
Fax:0086-898-63330673
CellP:0086-18889653800
Email: [email protected]
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