Data from the plastid genomes that have been completely sequenced reveal that introns are a general feature of these genomes. Each of the three classes of introns (groups I, II, and III) have a characteristic secondary structure that is related to the mechanisms by which the intervening sequence is excised from RNA precursors. The secondary structure requirements, along with other constraints, appear to limit the acceptance of mutational changes in intron sequences through evolutionary time. Group I introns, which were the first self-splicing introns identified (Zaug and Cech, 1980), are found in a single tRNA gene, trnL(UAA), from a number of plastid genomes. Group III introns have thus far only been identified in the euglenophytes Euglena gracilis and Astasia longa (Christopher and Hallick, 1989) and appear to be truncated (or streamlined) group II introns. It is noteworthy that group I introns are absent from the newly sequenced plastid genomes of Euglena gracilis (Hallick et al., 1993) and beechdrops, Epifagus virginiana (Wolfe et al., 1992). Both genomes are atypical, however: the Euglena genome is markedly different in structural organization and may have had a separate origin from the plastid genomes of land plants; beechdrops is a nonphotosynthetic parasitic plant, and its genome is highly reduced, lacking trnL (UAA) among other genes. Although comparative sequence analyses of both group I and group III introns could provide information about rates and mechanisms of chloroplast DNA evolution, there are few comparative data, and consequently our discussion will be limited to group II introns.
Group II introns form the most numerous and best characterized class of plastid intervening sequences. They are found in both protein-coding genes and tRNA genes. The secondary structure of group II introns is characterized by six domains (I–VI) (reviewed in Michel et al., 1989). Domain I has a complicated structure and contains sites that probably form base pairs with the 5' exon and are important for intron processing (Jacquier and Michel, 1987). Domains II–VI are typically simple stem–loop structures. Domains V and VI have also been shown to be required for proper processing of the transcript (Schmelzer and Müller, 1987; Jarrell et al., 1988). Learn et al. (1992) examined the evolutionary constraints on the various domains of group II introns in a comparative study of the intron found in a tRNA gene, trnV(UAC), from seven land plants. They found that domain II evolves most rapidly, comparable to the synonymous substitution rate of protein-coding genes, consistent with the finding that domain II may be dispensable in self-splicing introns (Kwakman et al., 1989). Portions of domain I (that are important in binding to the 5' exon) and domain V evolve at the slowest rates,