Complete Mitochondrial DNA Sequence of the Scallop Placopecten magellanicus: Evidence of Transposition Leading to an Uncharacteristically Large Mitochondrial Genome David R. Smith Æ Marlene Snyder Received: 24 June 2006 / Accepted: 6 July 2007 / Published online: 6 October 2007 Ó Springer Science+Business Media, LLC 2007 Abstract Complete sequence determination of the mito- chondrial (mt) genome of the sea scallop Placopecten magellanicus reveals a molecule radically different from that of the standard metazoan. With a minimum length of 30,680 nucleotides (nt; with one copy of a 1.4 kilobase (kb) repeat) and a maximum of 40,725 nt, it is the longest reported metazoan mitochondrial DNA (mtDNA). More than 50% of the genome is noncoding (NC), consisting of dispersed, imperfectly repeated sequences that are associ- ated with tRNAs or tRNA-like structures. Although the genes for atp8 and two tRNAs were not discovered, the genome still has the potential for encoding 46 genes (the additional genes are all tRNAs), 9 of which encode tRNAs for methionine. The coding portions appear to be evolving at a rate consistent with other members of the pectinid clade. When the NC regions containing ‘‘dispersed repeat families’’ are examined in detail, we reach the conclusion that transposition involving tRNAs or tRNA-like structures is occurring and is responsible for the large size and abundance of noncoding DNA in the molecule. The rarity of enlarged mt genomes in the face of a demonstration that they can exist suggests that a small, compact organization is an actively maintained feature of metazoan mtDNA. Keywords Placopecten magellanicus Á Mitochondrial genome Á Transposition Á Bivalve Á Mollusk Á Dispersed repeats Introduction Metazoan mitochondrial (mt) genomes were once consid- ered to be an extreme example of genetic economy (Attardi 1985) showing a highly reduced size of 15–17 kilobases (kb) and a gene content of only 13 protein coding-, 2 rRNA coding-, and 22 tRNA coding-genes. Although many of the reported animal mtDNAs fit this model, an increasing number seem to deviate from it substantially. For example, the mt genome of the snail Biomphalaria glabrata has a length of only 13.6 kb (Dejong et al. 2004); and those of three species of bark weevil, the brachiopod Lingula ana- tina, and the sea scallop Placopecten magellanicus can be as large as 36 kb, 28.8 kb, and 40 kb, respectively (Boyce et al. 1989; Endo et al. 2005; Snyder et al. 1987; Gjetvaj et al. 1992). The gene content of metazoan mtDNA has also been shown to deviate from what was considered the ‘‘standard’’ set. There are examples of genomes with multiple copies of either protein coding-, rRNA coding-, or tRNA coding-genes, and those which lack genes, such as atp8 and certain tRNAs (Hoffmann et al. 1992; Beagley et al. 1995; Yokobori et al. 2004; Endo et al. 2005; Mizi et al. 2005). There are numerous reports describing dupli- cations of large coding and NC regions (Rand 1993; Yokobori et al. 2004). Dispersed repeated sequences associated with tRNA-like structures have also been observed, raising the possibility of transposition within the mt compartment (Endo et al. 2005). Furthermore, the observations of heteroplasmy, recombination (Ladoukakis and Zouros 2001a,b), introns (Beagley et al. 1995), and Reviewing Editor: Gail Simmons D. R. Smith Á M. Snyder (&) Department of Biology, Acadia University, B4P 2R6 Wolfville, Nova Scotia, Canada e-mail: marlene.snyder@acadiau.ca D. R. Smith Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada 123 J Mol Evol (2007) 65:380–391 DOI 10.1007/s00239-007-9016-x