Photosynthesis takes place in chloroplasts, lens-shaped plastids found in green algae and higher plants. Chloroplasts originated from prokaryotic symbionts; they contain circular DNA molecules (chloroplast DNA (cpDNA)) in multiple copies that code for ∼100 genes or even less in certain species. Only a fraction of the enzymes active in chloroplasts is coded by cpDNA; nuclear genes control many functions and structures of chloroplasts. Accordingly, chloroplasts are semiautonomous cell organelles. Comparatively, low mutation rates and the uniparental inheritance (typically maternal in most angiosperms and paternal in gymnosperms) of cpDNA promote the investigation of cpDNA variation for phylogenetic and phylogeographic studies. Short cpDNA fragments are increasingly used for species identification based on molecular methods (DNA barcoding) in plants. Chloroplast transformation offers advantages with regard to biosafety issues for angiosperms in comparison to the genetic transformation of the nucleus since transgenes are less likely to escape via pollen.

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