Chloroplast Genome Sequence of Oil Palm (Elaeis guineensis Jacq.)

Oil palm (Elaeis guineensis Jacq.) is one of the most useful crops generating many economically important products. To better understand the molecular basis of oil palm chloroplasts, we have completed the oil palm chloroplast genome sequencing using the 454 pyrosequencer. The size of oil palm cp genome is 156,973 bp in length with a large single-copy region of 85,192 bp flanked by inverted repeats of 27,071 bp in each side. The two repeats were joined by a small single-copy region of 17,639 bp. The chloroplast genome annotation result showed 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. We observed 18 non-silent and 10 silent RNA editing events among 19 cp protein coding genes by aligning the cp genome sequence with total oil palm cDNA sequences.  An analysis of functional categories of oil palm chloroplast genome shows the differential expression between leave, fruit, and abscission zone. Photosynthesis gene categories and rubisco gene are function and highly express in leaves, while ribosomal proteins gene category is high express in fruits. Besides, most of genes are hardly express in abscission zone. The phylogenic tree of the chloroplast was conducted using fifty common chloroplast protein-coding genes from 33 plant taxa.  Their topologies are similar and strongly support for the position of Elaeis guineensis as the sister ofclosely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.