This subsequently led to the selection of cpDNA as one of the first candidates for complete genome sequencing. The presence of nucleic acids within chloroplasts was established in 1963. In particular, chloroplast gene expression machinery is a distinctive assembly of prokaryotic, eukaryotic, and phage-like components–likely the result of acquisition of a great number of regulatory proteins during evolution.
#Clc sequence viewer 7 phylogram scale full#
Chloroplasts possess their own genome and a full complement of transcriptional and translation machinery to express their genetic information. In addition to photosynthesis, other important metabolic activities take place within chloroplasts including the production of starch, certain amino acids and lipids, some of the colorful pigments in flowers, vitamins and several key aspects of sulfur and nitrogen metabolism. 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.Ĭhloroplasts are dynamic organelles of prokaryotic origin within the plant cell that house the photosynthetic apparatus.
Availability of a complete Citrus chloroplast genome sequence provides valuable information on intergenic spacer regions and endogenous regulatory sequences for chloroplast genetic engineering. 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. This is the first complete chloroplast genome sequence for a member of the Rutaceae and Sapindales. 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. 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. 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. 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. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. However, in Citrus the infA gene is absent. Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. 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). We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms.
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. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. 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.
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