While structure and coding capacity of the plastid genome are highly conserved among land plants, the plastome has experienced many architectural changes during the evolution of algae (Simpson and Stern 2002). The most dramatic change appears to have occurred in some dinoflagellates, where single genes are contained on small (2-3 kb) minicircles and the sum of the minicircles may make up the plastid genome (Zhang et al. 1999; Barbrook and Howe 2000). This unusual multipartite plastid genome structure seems to be confined to dinoflagellates: the genomes of most other algae map as circular molecules of 100-300 kb (Reith 1995; Simpson and Stern 2002).
The inverted repeat region present in most higher plant plastomes and containing the ribosomal RNA (rRNA) operon (3.1; Fig.1) has undergone many structural changes in algae. While, for example, many green and red algae have rRNA op-eron-containing IRs, some green and red algae have lost one of the IRs and, thus, possess only a single copy of the rRNA operon. Again other green and red algal species have direct repeats rather than inverted repeats (Reith 1995). The perhaps most unusual structure of the rRNA operon is found in Euglena gracilis, a unicellular flagellate-like protist with a green algal plastid acquired via secondary endo-symbiosis. In Euglena, multiple copies of the rRNA operon are arranged as a tandem array of three complete and one partial operons (Hallick et al. 1993).
The plastomes of algae also vary greatly with respect to gene density and information content. While in some algal lineages, plastid genomes are extremely compact and gene-dense (such as the plastome of the cryptophyte alga Guillardia theta with 180 genes in a genome of only 122 kb; Douglas and Penny 1999), genome expansion by accumulation of non-coding DNA has occurred in other algae. The model green alga Chlamydomonas reinhardtii provides a particularly striking example for such a genome expansion: its plastome is 203 kb large, but contains only 99 genes. The presence of repetitive DNA (i.e. short dispersed repeats) in in-tergenic regions accounts for more than 20% of the genome size (Maul et al. 2002). The selective forces that have led to extreme genome streamlining in some algae, but genome expansion in others are currently totally unknown.
Green algae share a common ancestry with land plants and it is therefore unsurprising that the gene content of their plastomes is similar to that of higher plants. Exceptions include, for example, petN which is nuclear encoded in green algae (Hager et al. 1999; Table 1), and two genes for proteins involved in plastid division which are present in the plastome of the green alga Chlorella vulgaris, but absent from the ptDNA of higher plants and another green alga, Chalmydomo-nas reinhardtii (Wakasugi et al. 1997). In contrast to green algae, the plastomes of non-green algae have retained many genes that are absent from the plastid genomes of land plants (Reith and Munholland 1993, 1995; Kowallik et al. 1995;
Reith 1995; Ohta et al. 2003). It is generally assumed that these additional genes were transferred to the nucleus in the common ancestor of land plants and green algae which, in this respect, represent a more derived state of plastome evolution. Among the algal plastomes fully sequenced to date, the red alga Porphyra purpurea has the highest number of genes (250 genes in a genome of 191 kb, Reith and Munholland 1995). Expansion of the two main gene classes in plastid genomes (photosynthesis genes and genetic system genes; see 3.2.1 and 3.2.2) as well as presence on the plastome of additional groups of genes (e.g. for amino acid, fatty acid, pigment and vitamin biosyntheses) account for this enlarged gene repertoire.
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