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Background  The Streptophyta comprise all land plants and six monophyletic groups of charophycean green algae. Phylogenetic analyses of four genes from three cellular compartments support the following branching order for these algal lineages: Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales and Charales, with the last lineage being sister to land plants. Comparative analyses of the  Mesostigma viride  (Mesostigmatales) and land plant chloroplast genome sequences revealed that this genome experienced many gene losses, intron insertions and gene rearrangements during the evolution of charophyceans. On the other hand, the chloroplast genome of  Chaetosphaeridium globosum  (Coleochaetales) is highly similar to its land plant counterparts in terms of gene content, intron composition and gene order, indicating that most of the features characteristic of land plant chloroplast DNA (cpDNA) were acquired from charophycean green algae. To gain further insight into when the highly conservative pattern displayed by land plant cpDNAs originated in the Streptophyta, we have determined the cpDNA sequences of the distantly related zygnematalean algae  Staurastrum punctulatum  and  Zygnema circumcarinatum .    Results  The 157,089 bp  Staurastrum  and 165,372 bp  Zygnema  cpDNAs encode 121 and 125 genes, respectively. Although both cpDNAs lack an rRNA-encoding inverted repeat (IR), they are substantially larger than  Chaetosphaeridium  and land plant cpDNAs. This increased size is explained by the expansion of intergenic spacers and introns. The  Staurastrum  and  Zygnema  genomes differ extensively from one another and from their streptophyte counterparts at the level of gene order, with the  Staurastrum  genome more closely resembling its land plant counterparts than does  Zygnema  cpDNA. Many intergenic regions in  Zygnema  cpDNA harbor tandem repeats. The introns in both  Staurastrum  (8 introns) and  Zygnema  (13 introns) cpDNAs represent subsets of those found in land plant cpDNAs. They represent 16 distinct insertion sites, only five of which are shared by the two zygnematalean genomes. Three of these insertions sites have not been identified in  Chaetosphaeridium  cpDNA.    Conclusion  The chloroplast genome experienced substantial changes in overall structure, gene order, and intron content during the evolution of the Zygnematales. Most of the features considered earlier as typical of land plant cpDNAs probably originated before the emergence of the Zygnematales and Coleochaetales.

bmc biology

The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales