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Background  In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs) deviate considerably from the ancestral pattern described for the prasinophyte  Nephroselmis olivacea , the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs.  Chlorella vulgaris  (Chlorellales) is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga  Leptosira terrestris  (Ctenocladales).    Results  The 195,081-bp  Leptosira  chloroplast genome resembles the 150,613-bp  Chlorella  genome in lacking a large inverted repeat (IR) but differs greatly in gene order. Six of the conserved genes present in  Chlorella  cpDNA are missing from the  Leptosira  gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs) account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in  Chlorella  but similar to that in the chlorophycean  Scenedesmus obliquus , the gene distribution is highly biased over the two DNA strands in  Leptosira . Nine genes, compared to only three in  Chlorella , have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the  rpoB  gene is fragmented into two ORFs. Short repeats account for 5.1% of the  Leptosira  genome sequence and are present mainly in intergenic regions.    Conclusion  Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate that the IR was lost on at least two separate occasions. The intriguing similarities of the derived features exhibited by  Leptosira  cpDNA and its chlorophycean counterparts suggest that the same evolutionary forces shaped the IR-lacking chloroplast genomes in these two algal lineages.

bmc genomics

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae