It is now generally recognized that intraspecific variation in cpDNA is relatively common; however, less is known about plastid genome variation within individuals. cpDNA chimeras (plants with different cpDNA genotypes) are well-known from variegated cultivars and may result from biparental inheritance or somatic mutations. We document here an example of intra-individual variation in plastid rDNA in a wild species, Cynomorium coccineum, a nonphotosynthetic holoparasite. PCR amplifications of all portions of the ribosomal DNA cistron (16S, 23S, 4.5S, 5S and intervening spacers) were made. The PCR products were cloned and the inserts sequenced from 19 colonies. Sequence variation has been observed for all portions of the cistron, however, we will here focus on variation in the large-subunit (LSU, 23S) rDNA which is 2.7 kb in length. Of the 19 clones, five distinct types were identified. Fifteen of the sequences were nearly identical (11 differences or less) and these were designated Type I. The remaining types (II-V) were each represented by a single clone and differed from Type I by 90-235 changes. Of the five types, Type I sequences were the most derived when compared with a tobacco outgroup sequence (range across Types 250-370 differences). Higher-order structures were constructed for representatives of the five Types to address questions of functionality. Major structural changes (mainly multiple base deletions relative to tobacco) were noted in the variable regions V2, V6, V12, V15, and V16. These deletions varied in size, and those of lesser magnitude retained sequences that were alignable with tobacco. Relatively few mutations were seen in the peptidyl transferase loop, thus suggesting retention of functionality. Given that the PCR products were obtained from total genomic DNA, it is not presently known whether heteroplasmy in Cynomorium derives from variation among cpDNAs of different plastids, cells or tissues within the individual plant.

Key words: 23S ribosomal DNA, heteroplasmy, parasitic plant, plastid