title: Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera).
abstract: 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.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
authors.forename: Ya-Yi
authors.initials: YY
authors.lastname: Huang
authors.forename: Antonius J M
authors.initials: AJ
authors.lastname: Matzke
authors.forename: Marjori
authors.initials: M
authors.lastname: Matzke
mesh_terms: D000926:Anticodon / Q000235:genetics; D001483:Base Sequence; D003059:Cocos / Q000235:genetics*; D003062:Codon / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics; D054628:Genome, Chloroplast / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011544:Pseudogenes / Q000235:genetics; D017393:RNA Editing / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D000926:Anticodon; D003062:Codon
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