Tandem integration of circular plasmid contributes significantly to the expanded mitochondrial genomes of the green-tide forming alga (Ulvophyceae, Chlorophyta).

Comparative mitogenomics of species have revealed remarkable variations in genome size due to the integration of exogenous DNA fragments, the proliferation of group I/II introns, and the change of repeat sequences. The genus is a species-rich taxonomic group, containing a variety of green-tide forming algae. In this study, five complete mitogenomes of the green-tide forming macroalga, R. Horimoto and S. Shimada, were assembled and compared with the available ulvophyceae mtDNAs. The main circular mitogenomes of ranged from 82.94 to 111.49 kb in size, and its 111.49-kb mitogenome was the largest mitogenome sequenced so far. The expansion of mitogenomes is mainly due to the tandem integration of a 5.36-kb mitochondrial circular plasmid (pUme), as well as the proliferation of introns. An intact DNA-directed RNA polymerase gene () was present in pUme of and was then detected in two putative plasmids (pUmu1 and pUmu2) found in . The observed integration of the circular plasmid into mitogenomes seems to occur homologous recombination, and is a more recent evolutionary event. Many highly homologous sequences of these three putative plasmids can be detected in the other mtDNAs sequenced thus far, indicating the integration of different mitochondrial plasmid DNA into the mitogenomes is a common phenomenon in the evolution of mitogenomes. The random incidence of destruction of plasmid-derived s and open reading frames (s) suggests that their existence is not the original characteristic of mitogenomes and there is no selective pressure to maintain their integrity. The frequent integration and rapid divergence of plasmid-derived sequences is one of the most important evolutionary forces to shape the diversity of mitogenomes.