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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 cryptomonad Guillardia theta Hill et Wetherbee and used gene signatures, predicted amino acid sequences, and gene arrangements for phylogenetic inferences. The Guillardia atpA cluster contains the genes atpI,H,G,F,D,A in the given order, thus reflecting the cyanobacterial/red algal/chromophyte gene arrangement. In addition, the order of both the upstream sequences rpoB,C1,C2,rps2,tsf and the downstream sequences ycf16/24, which is found exclusively in red algal chloroplast genomes, is conserved in Guillardia. This gene order, which presumably is the result of the reduction process of the cyanobacterial genome following primary endosymbiosis, provides strong evidence for a red algal ancestry of the Guillardia chloroplast and supports the hypothesis of secondary endosymbioses giving rise to chl 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 ATPase genes together with their upstream and downstream genes, is consistent with a single primary photosynthetic eukaryote that gave rise to all extant algal lineages and land plants by either direct filiation or secondary endosymbioses.