Evolution of length variation and heteroplasmy in the chloroplast rDNA of symbiotic dinoflagellates (Symbiodinium, Dinophyta) and a novel insertion in the universal core region of the large subunit rDNA

Marine dinoflagellates are a diverse and ecologically important group of unicellular protists responsible for events such as 'red tides' and for forming mutualistic symbioses with various invertebrates. However, little is known about the evolution of organellar DNA in these organisms. We analysed domain V of the chloroplast large subunit ribosomal DNA (cp23S-rDNA) from a variety of symbiotic dinoflagellates and uncovered several unique features. These included length heteroplasmy of cp23S-rDNA that resulted from deletion mutations and the presence of a 1-13 bp nucleotide insertion in the universal core region. The insertion in the large subunit rDNA is novel across all kingdoms and appears to be a unique derived state for the symbiotic genus Symbiodinium. In addition, analysis of expansion segments (ES) revealed that the cp23S-rDNA domain V of symbiotic dinoflagellates is the most size variable of any known plastid-harbouring organism. Our results demonstrate that the universal core secondary structure and the chloroplast rDNA ES are less constrained in size than previously thought.