MOLECULAR STRUCTURE AND EVOLUTION OF THE CHLOROPLAST atpB/E GENE CLUSTER IN THE DIATOM ODONTELLA SINENSIS

We cloned and sequenced the chloroplast atpB/E gene cluster encoding the β ‐ and εsubunits of the chloroplast ATPase, together with its flanking regions, in the centric diatom Odontella sinensis ( Grev.) Grunow. This gene cluster, which was transcribed into a main transcript of 3.5 kb, was flanked by the genes ycf 3 ( upstream atpB) and ORF 263 (downstream atpE), the latter being unknown from land plant chloroplasts. All reading frames were located on the same strand. In contrast to most higher plants , atpB and atpE in Odontella sinensis did not overlap but were separated from each other by 13 nucleotides (nts), similar to other chlorophyll a+c‐ containing algae. Comparisons of atpB/E spacer regions from cyanobacteria, algae, and land plants indicate that separated atpB and atpE genes reflect a primitive rather than derived character. The spacer separating atpE and ORF 263 contained an inverted repeat sequence of 14 nts. Comparisons of inferred amino acid sequences from atpB of Odontella with known ATPase‐β sequences from other photosynthetic organisms revealed 75–91% identical amino acid residues. In contrast, the εsubunits exhibited 26–65% protein sequence conservation, with sequence identities around 40% within chlorophyll a+ c ‐containing algae. Relative to β‐subunits ofchlorophjtes (including land plants) and cyanobacteria, a gap of four amino acid residues was found close to the N‐terminus of ATPase‐β in Odontella. Phylogenetic trees constructed by maximum parsimony and distance matrix methods were consistent with a monophyletic origin of all extant plastid types from within the cyanobacterial radiation, but did not unequivocally delineate evolutionary affiliations among nongreen plastids .