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Comparative Study
, 8 (8), e74736

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos Nucifera)

Comparative Study

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos Nucifera)

Ya-Yi Huang et al. PLoS One.


Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. Coconut chloroplast genome map.
Genes shown on the outside of the large circle are transcribed clockwise, while genes shown on the inside are transcribed counterclockwise. Thick lines of the small circle indicate IRs. Genes with intron are marked with “*”. Pseudo genes are marked with “Ψ”.
Figure 2
Figure 2. IR expansion into the LSC and SSC regions.
Comparison of IR boundaries among six palm species. Numbers in red denote distance between rpl22 and junction of LSC and IRB. Numbers in blue denote distance between rps19 and junction of LSC and IRA. Numbers in gray denote distance between psbA and junction of LSC and IRA.
Figure 3
Figure 3. Phylogenetic tree of monocots.
Numbers above/below the branches are bootstrap value (only values higher than 50% are shown). Black square denotes rps19 duplication, gray square denotes rps19 pseudogenization, white square denotes complete loss of duplicate rps19, and blue square denotes pseudo ycf1 and ndhF overlap.

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    1. Palmer J (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19: 325–354. - PubMed
    1. Yang M, Zhang X, Liu G, Yin Y, Chen K, et al. (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PloS ONE 5: e12762. - PMC - PubMed
    1. Uthaipaisanwong P, Chanprasert J, Shearman JR, Sangsrakru D, Yoocha T, et al. (2012) Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene 500: 172–180. - PubMed
    1. Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28: 583–600. - PubMed
    1. Cai Z, Penaflor C, Kuehl J, Leebens-Mack J, Carlson J, et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6: 77. - PMC - PubMed

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This work was funded by Academia Sinica ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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