Extensive DNA sequencing of the chloroplast genome of the red alga Porphyra purpurea has resulted in the detection of more than 125 genes. Fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. These include genes encoding 17 photosynthetic proteins, three tRNAs, and nine ribosomal proteins. In addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes encoding miscellaneous proteins are among those not known to be located on land plant chloroplast genomes. The increased coding capacity of the P. purpurea chloroplast genome, along with other characteristics such as the absence of introns and the consenration of ancestral operons, demonstrate the primitive nature of the f . purpurea chloroplast genome. In addition, evidence for a monophyletic origin of chloroplasts is suggested by the identification of two groups of genes that are clustered in chloroplast genomes but not in cyanobacteria.
INTRODUCTIONThe complete DNA sequences of three photosynthetic land plant chloroplast genomes have revealed an enormous amount of functional and evolutionary information. The chloroplast genomes of tobacco (Shinozaki et al., 1986), rice (Hiratsuka et al., 1989), and the liverwort Marchantia polymorpha (Ohyama et al., 1986) have each been shown to contain 110 to 118 genes. The products of these genes are primarily involved in two processes: gene expresssion (59 to 60 genes) and photosynthesis (29 genes). In addition, 11 genes encoding subunits of NADPH dehydrogenase (Arizmendi et al., 1992) as well as a number of conserved open reading frames (ORFs) are contained on these genomes. The gene content of all land plant chloroplast genomes investigated is surprisingly conserved (for review, see Palmer, 1991).Alga1 chloroplast genomes, on the other hand, have not been so extensively characterized. Current information on the chloroplast genomes of chlorophyll a/b-containing algae suggest that their gene content is not too different from that of land plants, although a few genes that are absent from land plant chloroplast genomes (e.g., tufA in several species [Baldauf et al., 19901, rpl5 [Christopher and Hallick, 19891, and ccsA [Orsat et al., 19921 in Euglena gracilis) have been identified. Of greater significance, however, may be the observation of substantial genome rearrangements in green alga1 chloroplast genomes in the form of the splitting up of ancestral operons in several species of Chlamydomonas (e.g., Woessner et al., 1987) and the large number of introns, including introns within introns, To whom correspondence should be addressed. in E. gracilis (Christopher and Hallick, 1989; Copertino and Hallick, 1991). These observations are indicative of chloroplast genomes that are evolving under more relaxed constraints than land plant chloroplast genomes. lnformation about the gene content of chloroplast genomes from chromophyte (chlorophyll a/c-containing) and rhodophyte/glaucophyte (c...