A family of selfish minicircular chromosomes with jumbled chloroplast genefragments from a dinoflagellate

Chloroplast genes of several dinoflagellate species are located on unigenic DNA minicircular chromosomes. We have now completely sequenced five aberra nt minicircular chromosomes from the dinoflagellate Heterocapsa triquetra. These probably nonfunctional DNA circles lack complete genes, with each bei ng composed of several short fragments of two or three different chloroplas t genes and a common conserved region with a tripartite 9G-9A-9G core like the putative replicon origin of functional single-gene circular chloroplast chromosomes. Their sequences imply that all five circles evolved by differ ential deletions and duplications from common ancestral circles bearing fra gments of four genes: psbA. psbC, 16S rRNA, and 23S rRNA. It appears that r ecombination between separate unigenic chromosomes initially gave intermedi ate heterodimers, which were subsequently stabilized by deletions that incl uded part or all of one putative replicon origin. We suggest that homologou s recombination at the 9G-9A-9G core regions produced a psbA/psbC heterodim er which generated two distinct chimeric circles by differential deletions and duplications. A 23S/16S rRNA heterodimer more likely formed by illegiti mate recombination between 16S and 23S rRNA genes. Homologous recombination between the 9G-9A-9G core regions of both heterodimers and additional diff erential deletions and duplications could then have yielded the other three circles. Near identity of the gene fragments and 9G-9A-9G cores, despite d iverging adjacent regions, may be maintained by gene cony version. The cons erved organization of the 9G-9A-9G cores alone favors the idea that they ar e replicon origins and suggests that they may enable the aberrant minicircl es to parasitize the chloroplast's replication machinery as selfish circles .