A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

Abstract

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...

Comparative Analysis of the Complete Plastid Genome Sequence of the Red Alga Gracilaria tenuistipitata var. liui Provides Insights into the Evolution of Rhodoplasts and Their Relationship to Other Plastids

“…In contrast, the red lineage contains many genes that are not located on the plastid genome of green plants. Rhodophyte plastid genomes have an increased coding capacity (Reith and Munholland 1993), often containing more than twice the number of genes (232-251) common to species of the green lineage. The secondary plastids in the red lineage also encode a large number of genes (174-183), but not as many as in the primary plastids.…”

“…In the red lineage, large repeats are absent in Gracilaria and in the Cyanidiales genera Cyanidium and Cyanidioschyzon. Porphyra purpurea has direct nonidentical repeats containing only the rRNA genes (Reith and Munholland 1993). The plastid genomes of other red algae have been mapped.…”

Organisation of the plastid genome from the rhodophyteChondrus crispus(Gigartinales); sequence and phylogeny of the 16S rRNA gene

“…The three other red algal genomes which have been characterised are also fairly large: 178 kb for Griffthsia pacifica (Li & Cattolico, 1987), 185 kb for Porphyra yezoensis (Shivji, 1991) and 188 kb for Porphyra purpurea (Reith & Munholland, 1993a). This large size is coincident with an increased number of encoded genes relative to landplant chloroplast genomes (Reith & Munholland, 1993a). Fragment denomination is explained in Table 2.…”

“…The chloroplast genomes of the liverwort Marchantia polymorpha L. (Ohyama et al, 1986), tobacco (Shinozaki et al, 1986) and rice (Hiratsuka et al, 1989) have been completely sequenced. Recently, extensive sequencing of the chloroplast genome of the red alga Porphyra purpurea (Roth) Agardh has shown the presence of more than I25 genes, 46% of which are not found in the chloroplast genomes of land plants (Reith & Munholland, 1993a). Two other red algal chloroplast genomes have been analysed: those of a florideophyte species, sequence of Cyanidium caldarium IGaldieria sulphuraria (Galdieri) Merola; Maid & Zetsche, 1990] as the sole representative of red algae.…”

Complete Sequence of the Mitochondrial DNA of the Red Alga Porphyra purpurea: Cyanobacterial Introns and Shared Ancestry of Red and Green Algae

“…These findings raise questions about the homogeneity of the DNA material that was used for constructing the clone library. For mtDNA extraction, gametophytes (folious thalli) of P. purpurea were collected in the wild, offshore Nova Scotia, Canada, and propagated in the laboratory (Reith and Munholland, 1993a). The observed variance in the sequenced DNA material suggests a considerable heterogeneity of the mitochondrial genome within cross-fertilizing populations of P. purpurea.…”