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Background   Dunaliella salina  Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because  D. salina  can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of  D. salina  have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of  D. salina  and compares them with those of the model green algae  Chlamydomonas reinhardtii  and  Volvox carteri .    Results  The  D. salina  organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the  D. salina  plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the  D. salina  ptDNA.    Conclusions  These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of  D. salina  and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the  D. salina  organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming  D. salina  nuclear genome sequence, placing  D. salina  in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA