Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships |
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Authors: | Tangphatsornruang Sithichoke Uthaipaisanwong Pichahpuk Sangsrakru Duangjai Chanprasert Juntima Yoocha Thippawan Jomchai Nukoon Tragoonrung Somvong |
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Affiliation: | National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand. sithichoke.tan@biotec.or.th |
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Abstract: | Rubber tree (Hevea brasiliensis) is an economical plant and widely grown for natural rubber production. However, genomic research of rubber tree has lagged behind other species in the Euphorbiaceae family. We report the complete chloroplast genome sequence of rubber tree as being 161,191 bp in length including a pair of inverted repeats of 26,810 bp separated by a small single copy region of 18,362 bp and a large single copy region of 89,209 bp. The chloroplast genome contains 112 unique genes, 16 of which are duplicated in the inverted repeat. Of the 112 unique genes, 78 are predicted protein-coding genes, 4 are ribosomal RNA genes and 30 are tRNA genes. Relative to other plant chloroplast genomes, we observed a unique rearrangement in the rubber tree chloroplast genome: a 30-kb inversion between the trnE(UUC)-trnS(GCU) and the trnT(GGU)-trnR(UCU). A comparison between the rubber tree chloroplast genes and cDNA sequences revealed 51 RNA editing sites in which most (48 sites) were located in 26 protein coding genes and the other 3 sites were in introns. Phylogenetic analysis based on chloroplast genes demonstrated a close relationship between Hevea and Manihot in Euphorbiaceae and provided a strong support for a monophyletic group of the eurosid I. |
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Keywords: | bp, base pair cp, chloroplast IDP, Isopentenyl diphosphate MVA, Mevalonate MEP, 1-Deoxy-D-xylulose 5-phosphate/2-C-methyl-D-erythritol 4-phosphate H. brasiliensis, Hevea brasiliensis PCR, Polymerase chain reaction RCA, Rolling cycle amplification ML, Maximum likelihood MP, Maximum parsimony TBR, Tree bisection and reconnection A, Adenosine C, Cytidine I, Inosine U, Uridine G, Guanosine LSC, Large single copy SSC, Small single copy IR, Inverted repeat ycf, Hypothetical chloroplast open reading frame EST, Expressed sequence tag |
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