Mitogenomics reveals a remarkably high intra-species substitution rate in the ascidian Botryllus schlosseri

The leitmotiv of mitochondrial genome (mtDNA) evolution in ascidians is the hypervariability of many genomic features (such as gene order, nucleotide substitution rate and tRNA gene content) even at short phylogenetic distances. As consequence, the ascidian mtDNA has been proved to unambiguously discriminate between two cryptic species of Ciona intestinalis. Here, we describe the mtDNA of a model species, the colonial ascidian Botryllus schlosseri. Two specimens, one from California and one from Italy, have been sequenced. We found that the mtDNA of B. schlosseri has a novel gene order, completely different from other ascidians, and encodes for peculiar tRNAlike structures. Surprisingly, the sequence divergence between the two specimens is up to one order of magnitude higher (depending on the functional mt region) than the one measured in other ascidian intra-species comparisons. However, this value is lower than the one measured within genera, and between the two cryptic C. intestinalis species. Thus, based on mtDNA, the Californian and Italian B. schlosseri specimens appear to belong to a single species that is characterized by a remarkably high nucleotide substitution rate.