Chloroplast genome organization in Chlamydomonas

Although the chloroplast genome of Chlamydomonas reinhardtii contains essentially the same complement of genes as chloroplast genomes of land plants, the arrangement of these genes within the circular DNA molecule is very different. Studies in several laboratories suggest that comparison of gene order, restriction fragment length polymorphisms, and sequences within chloroplast DNA may be valuable tools in phylogenetic analysis of Chlamydomonas species. We have found that six interfertile strains in the C. reinhardtii group differ by restriction fragment length polymorphisms throughout their chloroplast genomes. In two of these strains the chloroplast genomes are known to be colinear and the differences largely attributable to variations in the size and distribution of clusters of short dispersed repeat sequences occurring in intergenic regions. These repeats, which are marked by Aat II and Kpn I restriction sites, are present in the chloroplast genomes of all six interfertile strains of the C. reinhardtii group, but are absent from the chloroplast genomes of C. eugametos, C. moewusii, C. incerta and C. globosa. The latter two species, which are sensitive to the same vegetative cell autolysin as C. reinhardtii, do not appear to be interfertile with C. reinhardtii. Restriction fragment analysis of chloroplast DNA suggests that C. incerta and C. globosa are very similar to one another, but differ greatly from C. reinhardtii.