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Background  The production of  Citrus , the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease  Citrus  canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the  Citrus  chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms.    Results  The complete chloroplast genome sequence of  Citrus sinensis  is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs). Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in  Citrus  the  infA  gene is absent. The inverted repeat region has expanded to duplicate  rps19  and the first 84 amino acids of  rpl22 . The  rpl22  gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in  petL ,  psbH ,  ycf2  and  ndhA . Phylogenetic analyses using maximum parsimony (MP) and maximum likelihood (ML) methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of  Amborella  and Nymphaeales, relationship of the magnoliid genus  Calycanthus , and the monophyly of the eurosid I clade. Both MP and ML trees provide strong support for the monophyly of eurosids II and for the placement of  Citrus  (Sapindales) sister to a clade including the Malvales/Brassicales.    Conclusion  This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. Expansion of the inverted repeat region to include  rps19  and part of  rpl22  and presence of two truncated copies of  rpl22  is unusual among sequenced chloroplast genomes. Availability of a complete  Citrus  chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales.

bmc plant biology

The complete chloroplast genome sequence of Citrus sinensis(L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms