The Cephalopod Loligo bleekeri Mitochondrial Genome: Multiplied Noncoding Regions and Transposition of tRNA Genes Kozo Tomita, 1,* Shin-ichi Yokobori, 2 Tairo Oshima, 2 Takuya Ueda, 3 Kimitsuna Watanabe 1,3 1 Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan 2 Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan 3 Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Received: 9 May 2001 / Accepted: 3 October 2001 Abstract. We previously reported the sequence of a 9260-bp fragment of mitochondrial (mt) DNA of the cephalopod Loligo bleekeri [J. Sasuga et al. (1999) J. Mol. Evol. 48:692–702]. To clarify further the character- istics of Loligo mtDNA, we have sequenced an 8148-bp fragment to reveal the complete mt genome sequence. Loligo mtDNA is 17,211 bp long and possesses a stan- dard set of metazoan mt genes. Its gene arrangement is not identical to any other metazoan mt gene arrangement reported so far. Three of the 19 noncoding regions longer than 10 bp are 515, 507, and 509 bp long, and their sequences are nearly identical, suggesting that multipli- cation of these noncoding regions occurred in an ances- tral Loligo mt genome. Comparison of the gene arrange- ments of Loligo, Katharina tunicata, and Littorina saxatilis mt genomes revealed that 17 tRNA genes of the Loligo mt genome are adjacent to noncoding regions. A majority (15 tRNA genes) of their counterparts is found in two tRNA gene clusters of the Katharina mt genome. Therefore, the Loligo mt genome (17 tRNA genes) may have spread over the genome, and this may have been coupled with the multiplication of the noncoding regions. Maximum likelihood analysis of mt protein genes sup- ports the clade Mollusca + Annelida + Brachiopoda but fails to infer the relationships among Katharina, Loligo, and three gastropod species. Key words: Cephalopod Loligo bleekeri — Mito- chondrial DNA — Molluscan phylogeny — Gene rear- rangement — Noncoding region — tRNA Introduction Typical metazoan mitochondrial (mt) genomes are cir- cular, are 14–18 kb in size, and encode 13 protein, 2 rRNA [small and large subunit rRNAs (rrnS and rrnL)], and 22 tRNA (trnA, trnC, etc.) genes but no introns (Wolstenholme 1992; Boore 1999). The 13 polypeptides are involved in ATP synthesis coupled with electron transfer during O 2 consumption [ATP synthetase sub- units 6 and 8 (atp6 and atp8), cytochrome oxidase sub- units I–III (cox1–cox3), apocytochrome b (cob), and NADH dehydrogenase subunits 1–6 and 4L (nad1-6 and nad4L)]. Although the mt gene order is well conserved in several phyla (e.g., Arthropoda and Vertebrata), large variations in mt genome structure have been found within and between several specific groups of Mollusca. Complete mtDNA sequences have been reported for various mollusks: a polyplacophoran [Katharina tuni- cata (Boore and Brown 1994)] and three gastropods, Cepaea nemoralis [Pulmonata (Terrett et al. 1996; Yamazaki et al. 1997)], Albinaria coerulea [Pulmonata *Present address: Department of Biochemistry, University of Wash- ington, Seattle, WA 98195-7350, USA Correspondence to: Shin-ichi Yokobori; email : yokobori@ ls.toyaku.ac.jp J Mol Evol (2002) 54:486–500 DOI: 10.1007/s00239-001-0039-4 © Springer-Verlag New York Inc. 2002