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Genetics, Vol. 167, 835-850, June 2004, Copyright © 2004
doi:10.1534/genetics.103.026187
Evidence That the Large Noncoding Sequence Is the Main Control Region of Maternally and Paternally Transmitted Mitochondrial Genomes of the Marine Mussel (Mytilus spp.)
Liqin Cao*,
Ellen Kenchington*,
,
Eleftherios Zouros
and
George C. Rodakis
,1
* Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
Department of Fisheries and Oceans, Dartmouth, Nova Scotia B2Y 4A2, Canada
Department of Biology, University of Crete, 71409 Heraklion, Crete, Greece
Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
1 Corresponding author: Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15701 Athens, Greece.
E-mail: grodakis{at}biol.uoa.gr
Both the maternal (F-type) and paternal (M-type) mitochondrial genomes of the Mytilus species complex M. edulis/galloprovincialis contain a noncoding sequence between the l-rRNA and the tRNATyr genes, here called the large unassigned region (LUR). The LUR, which is shorter in M genomes, is capable of forming secondary structures and contains motifs of significant sequence similarity with elements known to have specific functions in the sea urchin and the mammalian control region. Such features are not present in other noncoding regions of the F or M Mytilus mtDNA. The LUR can be divided on the basis of indels and nucleotide variation in three domains, which is reminiscent of the tripartite structure of the mammalian control region. These features suggest that the LUR is the main control region of the Mytilus mitochondrial genome. The middle domain has diverged by only 1.5% between F and M genomes, while the average divergence over the whole molecule is 
20%. In contrast, the first domain is among the most divergent parts of the genome. This suggests that different parts of the LUR are under different selection constraints that are also different from those acting on the coding parts of the molecule.
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