EXTENSIVE GENE REARRANGEMENTS IN THE CHLOROPLAST DNAS OF CHLAMYDOMONAS SPECIES FEATURING MULTIPLE DISPERSED REPEATS

We have constructed a physical and gene map for the chloroplast DNA (c pDNA) of the unicellular green alga Chlamydomonas gelatinosa, a close relative of Chlamydomonas reinhardtii. At 285 kb, the C. gelatinosa cp DNA is 89 kb larger than its C. reinhardtii counterpart. The alteratio ns in the order of 77 genes on the cpDNAs of these green algae are att ributable to nine inversions and one event of expansion/contraction of the inverted repeat. These rearrangements are much more extensive tha n those previously reported between the cpDNAs of the closely related Chlamydomonas moewusii and Chlamydomonas pitschmannii. Because the div ergence level of the C. gelatinosa and C. reinhardtii chloroplast-enco ded large subunit rRNA gene sequences is equivalent to that of the cor responding C. moewusii and C. pitschmannii sequences, our results may suggest that, in the same period of time, there have been more numerou s rearrangements in the lineage comprising C. gelatinosa and C. reinha rdtii than in the lineage comprising C. moewusii and C. pitschmannii. Alternatively, given that substitution rates in chloroplast genes are not necessarily uniform across lineages, the extensive rearrangements between the C. gelatinosa and C. reinhardtii cpDNAs may reflect a long er divergence period for this pair of Chlamydomonas species compared t o that for the C. moewusii/C. pitschmannii pair. We have also found th at, like its C. reinhardtii homologue but unlike its C. moewusii and C . pitschmannii counterparts, the C. gelatinosa cpDNA features a large number of dispersed repeated sequences that are readily detectable by Southern blot hybridization with homologous fragment probes. Assuming that the two pairs of closely related Chlamydomonas species diverged a t about the same time, these data suggest that the susceptibility of C hlamydomonas cpDNAs to rearrangements is correlated with the abundance of repeated sequences. Preliminary characterization of a 345-bp C. ge latinosa cpDNA region containing a repeated sequence by both DNA seque ncing and Southern blot analysis has revealed no sequence homology bet ween this region and the cpDNAs of C. reinhardtii and other Chlamydomo nas species.