http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982566 MITOGENOME ANNOUNCEMENT The complete mitochondrial genome of the endangered spotback skate, Atlantoraja castelnaui Drew J. L. Duckett and Gavin J. P. Naylor Hollings Marine Laboratory, College of Charleston, Charleston, SC, USA Abstract Chondrichthyes are a highly threatened class of organisms, largely due to overfishing and other human activities. The present study describes the complete mitochondrial genome (16,750 bp) of the endangered spotback skate, Atlantoraja castelnaui. The mitogenome is arranged in a typical vertebrate fashion, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Keywords Chondrichthyes, elasmobranchs, long-PCR, mitogenome, next-generation sequencing History Received 7 October 2014 Accepted 27 October 2014 Published online 24 November 2014 The spotback skate, Atlantoraja castelnaui, is a large skate found along the coasts of Argentina, Uruguay and southern Brazil. It is the largest species of its genus, occupying waters greater than 24 m in depth and feeding on teleost fishes, cephalopods, decapods and other elasmobranchs (Barbini & Lucifora, 2012; Oddone & Amorim, 2007). Atlantoraja castelnaui is oviparous, with females depositing eggs on the ocean floor year round (Colonello et al., 2012; Oddone et al., 2008). Heavy fishing pressure in its native region has caused the decline of A. castelnaui, and it is currently listed as an endangered species (Hozbor et al., 2004). Improved knowledge of the mitochondrial genome of A. castelnaui will contribute to a better understanding of the species and provide a starting point for genetic studies that will benefit its conservation. The present study describes the complete mitochondrial genome of A. castelnaui using a juvenile male caught off the coast of Buenos Aires, Argentina in 2008. The species identifi- cation was confirmed through mitochondrial ND2 sequencing, as described in Naylor et al. (2012). The complete mitochondrial sequence was obtained through a combination of long-PCR and next-generation sequencing as in Yang & Naylor (2014), and the sequence was annotated using MitoAnnotator (Tokyo, Japan), a web-based tool for annotating fish mitogenomes (Iwasaki et al., 2013). The A. castelnaui mitogenome (GenBank Accession Number: KM507724) consisted of 16,750 bp with organization typical of vertebrate mitogenomes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region (Table 1). Twenty-nine of the 38 elements were encoded on the heavy strand, and ND6 was the only protein-coding gene encoded on the light strand. Sequence length varied from 168 bp (ATP8) to 1836 bp (ND5) in protein-coding genes and from 67 bp (tRNA Ser(GCU) ) to 75 bp (tRNA Leu(UAA) ) in tRNA genes. rRNA genes were 962 bp and 1680 bp in length for 12S and 16S Correspondence: Drew Duckett, Hollings Marine Laboratory, College of Charleston, 331 Fort Johnson Road, Charleston, SC 29412, USA. E-mail: duckettdj@g.cofc.edu Table 1. Characteristics of the mitochondrial genome of the spotback skate, Atlantoraja castelnaui. Gene/Element Start End Length (bp) Intergenic nucleotides* Start codon Stop codon Strand# tRNA Phe 1 69 69 H 12S rRNA 70 1031 962 H tRNA Val 1032 1103 72 H 16S rRNA 1104 2783 1680 H tRNA Leu(UAA) 2784 2858 75 H ND1 2859 3833 975 ATG TAA H tRNA Ile 3834 3903 70 H tRNA Gln 3903 3974 72 1 L tRNA Met 3975 4043 69 H ND2 4044 5089 1046 ATG TA– H tRNA Trp 5090 5158 69 H tRNA Ala 5160 5228 69 1 L tRNA Asn 5229 5301 73 L tRNA Cys 5335 5401 67 33 L tRNA Tyr 5402 5471 70 L COI 5473 7029 1557 1 GTG TAA H tRNA Ser(UGA) 7030 7100 71 L tRNA Asp 7101 7168 68 H COII 7172 7862 691 3 ATG T– – H tRNA Lys 7863 7936 74 H ATP8 7938 8105 168 1 ATG TAA H ATP6 8096 8779 684 10 ATG TAA H COIII 8782 9567 786 2 ATG TAA H tRNA Gly 9569 9638 70 1 H ND3 9639 9987 349 ATG T– – H tRNA Arg 9988 10,056 69 H ND4L 10,057 10,353 297 ATG TAA H ND4 10,347 11,727 1381 7 ATG T– – H tRNA His 11,728 11,796 69 H tRNA Ser(GCU) 11,797 11,863 67 H tRNA Leu(UAG) 11,864 11,935 72 H ND5 11,936 13,771 1836 ATG TAA H ND6 13,768 14,286 519 4 ATG TAG L tRNA Glu 14,288 14,356 69 1 L CytB 14,360 15,502 1143 3 ATG TAA H tRNA Thr 15,506 15,577 72 3 H tRNA Pro 15,586 15,654 69 8 L Control Region 15,655 16,750 1096 H #H and L denote heavy and light strands, respectively. *Values correspond to the number of nucleotides separating elements. Negative numbers indicate overlapping nucleotides between adjacent elements. Mitochondrial DNA Downloaded from informahealthcare.com by College Of Charleston on 11/25/14 For personal use only.