The complete sequencing of two plastid genomes more than twenty years ago (Ohyama et al. 1986; Shinozaki et al. 1986) marks a milestone in structural genomics and has had a profound influence on our understanding of the genetics and molecular biology of plastids. In the following years, dozens of additional plastid genomes have been sequenced. The 88 plastomes fully sequenced by the end of 2006 (http://www.ncbi.nlm.nih.gov/genomes/static/euk o.html) represent all major lineages of plant evolution. The picture that has emerged from these studies is that the plastome of land plants is a conservative genome while considerable variation in genome organization and coding capacity exists in algae (see 3.2.5).
In general, plastid genomes have a low GC content which is typically in the range of 30-40% (Ohyama et al. 1988; Shimada and Sugiura 1991). The low GC content is particularly pronounced in non-coding intergenic spacer regions where AT richness is often extreme and can reach values above 80% AT (Ohyama et al. 1988). Within coding regions, AT richness manifests as strong bias in codon usage, in that synonymous codons with an A or T in third codon position are strongly preferred over those with G or C in third position (Shimada and Sugiura 1991).
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