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Abstract
I have examined the linear arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber appear essentially identical in gross sequence arrangement. They share with the corn chloroplast genome a large inversion of 55 kilobases relative to the genomes of three legumes, mung bean, pea and broad bean. In addition there is one other rearrangement, a second, smaller inversion within the 55 kilobase inversion, which is specific to the corn genome. These two mutations are the only detected rearrangements among the five species (corn, spinach, petunia, cucumber and mung bean) examined whose chloroplast genomes contain a large inverted repeat sequence of 22-25 kilobases. Extensive sequence rearrangements are found in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus, there is a much more dynamic arrangement of sequences in those genomes that have lost the inverted repeat than in those which retain it.
Analysis of chloroplast DNA restriction patterns yields information relevant not only to the nature of change in the chloroplast genome but also to phylogenetic relationships among species. Small deletions (50-1000 base pairs) occur throughout the chloroplast genome, both symmetrically within the inverted repeat and asymmetrically at its ends, and also may occur in different regions within genes. Base substitutions which change restriction sites can be used as phylogenetic markers in order to recognize patterns of evolutionary relatedness among species. A case study in the genus Lycopersicon is presented.
