http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1060472 MITOGENOME ANNOUNCEMENT Complete mitochondrial genomes for Icelus spatula, Aspidophoroides olrikii and Leptoclinus maculatus: pan-Arctic marine fishes from Canadian waters Taylor Swanburg, John B. Horne, Shauna Baillie, Stanley D. King, Meghan C. McBride, Michael P. Mackley, Ian G. Paterson, Ian R. Bradbury, and Paul Bentzen Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada Abstract Three Arctic marine fishes Icelus spatula, Aspidophoroides olrikii and Leptoclinus maculatus have been identified as target species for investigating the effects of ocean warming on population patterns in high-latitude marine habitats around Canada. In preparation for this research, we have resolved whole mitochondrial genome sequences of 16 384, 17 200 and 16 384 bp for each species, respectively. GC content for each species was 47.5%, 44.2% and 45.3%, respectively. Mitogenome gene composition included 13 protein-encoding genes, 2 rRNA and 22 tRNA genes, for I. spatula and L. maculatus, consistent with other teleosts. Only 20 tRNA genes were annotated for A. olrikii, because tRNA-Pro and tRNA-Thr are poorly characterized and aberrantly located in this species. Keywords Agonidae, Cottidae, Stichaeidae, tRNA gene rearrangements History Received 5 June 2015 Accepted 6 June 2015 Published online 30 June 2015 The spatulate sculpin (Icelus spatula), Arctic alligatorfish (Aspidophoroides olrikii) and daubed shanny (Leptoclinus maculatus) are widely distributed Arctic fish species found on soft substrates at depths of 10–600 m (Robins & Ray, 1986). Associated with water temperatures approximating 0  C, the distributions of these cold-water species are expected to recede northward as global sea-temperatures increase, restricting avail- able habitat (Rose, 2005). This large-scale range shift is expected to disrupt longstanding patterns of gene flow, species dispersal and effective population sizes (Perry et al., 2005). Whole mitochondrial genome studies of northern-Canadian teleosts can be used to assess the effect of climate change on populations by inferring historical demographic changes and documenting present-day population patterns that can serve as a baseline for future research. To this end, we sequenced the mitogenomes of the three target species. Tissue samples were collected from the Beaufort Sea, Chukchi Sea and Hudson Strait, using bottom trawls on expeditions taking place in 2008 and 2009. Genomic DNA was extracted following Elphinstone et al. (2003). An input of 1 ng of genomic DNA was used in Illumina Nextera XT Library Preparation kit (Illumina Inc., San Diego, CA). DNA was tagged and fragmented by the Nextera XT transposome, followed by limited-cycle PCR amplification, AMPure XP magnetic-bead purification (Agencourt Bioscience Corporation, Beverly, MA) and the Illumina Nextera XT bead-based normalization protocol. The DNA library was sequenced using an Illumina MiSeq Benchtop Sequencer (San Diego, CA). Mitochondrial genome assembly from paired-end reads was conducted using MITObim 1.7 (Hahn et al., 2013), and MIRA 4.0 (Chevreux et al., 1999), using three GenBank references: Enophrys diceraus (NC_022147.1), Cottus dzungaricus (NC_024739.1) and Pholis crassispinna (NC_004410.1). Mitogenomes were annotated using two methods. First, in GENEIOUS 8.0.5 (Kearse et al., 2012; Biomatters, Ltd., Auckland, NZ) using the same GenBank references. Secondly, using the MitoFish online annotation pipeline (Iwasaki et al., 2013) and ARAGORN 1.2.36 (Laslett & Canback, 2004), for tRNA detection. Whole, annotated mitogenome sequences for I. spatula, A. olrikii and L. maculatus were deposited in GenBank under accession numbers: KT004432, KT004434 and KT004433, respectively. Total length and GC content were: 16384 bp and 47.5%; 17 200 bp and 44.2%; 16 384 bp and 45.3%, for each species, respectively. For I. spatula and L. maculatus, 13 protein- encoding, 2 rRNA and 22 tRNA genes were detected. However, for A. olrikii, tRNA-Pro and tRNA-Thr genes were not detected at the 5 0 end of the D-loop region, as is typical in teleosts. Instead, the MitoFish annotator places tRNA-Pro between ND5 and ND6 and tRNA-Thr in the middle of the 16S rRNA gene. The ARAGORN tRNA annotator did not detect either aberrant tRNA gene in A. olrikii. Pairwise sequence alignment suggests that tRNA-Pro is indeed at the 3 0 end of ND5, on the opposite strand, but has 5 90% homology with a reference from the same teleost order. Elements of the tRNA-Thr gene are found both within 16S rRNA and at the 5 0 end of D-loop but homology to references was poor. Neither tRNA gene was included as an annotation on the GenBank submission. The phylogenetic relationships of the three target species, assembly references and six other fish taxa from GenBank (accession numbers: NC_003174.1, NC_004299.1, NC_004404.1, NC_021459.1, NC_025242.1, NC_023475.1), were reconstructed Correspondence: Paul Bentzen, Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia B3H 4J1, Canada. Tel: +1 902 494 1105. E-mail: paul.bentzen@dal.ca Mitochondrial DNA Downloaded from informahealthcare.com by Dalhousie University on 06/30/15 For personal use only.