Analysis of a plastid gene cluster reveals a close relationship between Cyanidioschyzon and Cyanidium

Cyanidioschyzon merolae and Cyanidium caldarium are representative species among of the most primitive algae, although the two species are distinctly different in various morphological traits. We determined the nucleotide sequence of the rbcL gene and a flanking 8-kb region in the plastid genome of each of these algae. In both algae, 12 genes were identified in this region, in an identical order. This gene order is not conserved in the plastid genomes of other species of the kingdom Plantae that have been sequenced to date, An additional unidentified open reading frame was also found in the two algae that we analyzed, which has not been described in any other species of algae including Porphyra purpurea. Comparison of the amino acid sequences of selected genes also supported the conclusion that Cyanidioschyzon merolae and Cyanidium caldarium are closely related and that they are distinct from other rhodophytes.