The atpA gene cluster of Guillardia theta (Cryptophyta): A piece in the puzzle of chloroplast genome evolution

We cloned and sequenced the genes of the atpA (atp1) cluster, together with its upstream and downstream sequences, of the chloroplast genome of the cr yptomonad Guillardia theta Hill et Wetherbee and used gene signatures, pred icted amino acid sequences, and gene arrangements for phylogenetic inferenc es. The Guillardia atpA cluster contains the genes atpI,H,G,F,D,A in the gi ven order, thus reflecting the cyanobacterial/red algal/chromophyte gene ar rangement. In addition, the order of both the upstream sequences rpoB,C-1,C -2,rps2,tsf and the downstream sequences ycf 16/24, which is found exclusiv ely in red algal chloroplast genomes, is conserved in Guillardia. This gene order, which presumably is the result of the reduction process of the cyan obacterial genome following primary endosymbiosis, provides strong evidence for a red algal ancestry of the Guillardia chloroplast and supports the hy pothesis of secondary endosymbioses giving rise to chi a+c-containing algae . The close evolutionary relationship of the chloroplasts of Guillardia and red algae is furthermore supported by the lack of introns, high degrees of sequence similarities, and additional gene signatures, including spacers, gene overlaps, and inverted repeats. Gene cluster analysis, including the A TPase genes together with their upstream and downstream genes, is consisten t with a single primary photosynthetic eukaryote that gave rise to all exta nt algal lineages and land plants by either direct filiation or secondary e ndosymbioses.