STRUCTURE AND EVOLUTION OF THE LARGEST CHLOROPLAST GENE (ORF2280) - INTERNAL PLASTICITY AND MULTIPLE GENE LOSS DURING ANGIOSPERM EVOLUTION

We have determined the nucleotide sequence of the Pelargonium x hortor um ORF2280 homolog, the largest gene in the plastid genome of most lan d plants, and compared it to published homologs from Nicotiana tabacum , Epifagus virginiana, Spinacia oleracea, and Marchantia polymorpha. M ultiple alignment of protein sequences requires an extraordinary numbe r of gaps, indicating a very high frequency of insertion/deletion even ts during the evolution of the protein; however, the overall predicted size of the protein varies relatively little among the five species. At 2109 codons, the Pelargonium gene is smaller than other land plant ORF2280 homologs and exhibits a rate of nucleotide substitution severa l times higher relative to Nicotiana, Epifagus, and Spinacia. Southern -blot and restriction-mapping studies were carried out to uncover leng th variation in ORF2280 homologs from 279 species (representing 111 fa milies) of angiosperms. In many independent angiosperm lineages, this gene has sustained deletions ranging in size from 200 bp to almost 6 k b. Based on the severity of deletions, we postulate that the chloropla st homolog of ORF2280 has become nonfunctional in at least four indepe ndent lineages of angiosperms.