http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1030632 MITOGENOME ANNOUNCEMENT Mitogenomic sequence and phylogenetic placement of the Hortle’s whipray Himantura hortlei (Elasmobranchii: Dasyatidae) Hayley M. DeHart, Lei Yang, and Gavin J.P. Naylor Hollings Marine Laboratory, College of Charleston, Charleston, SC, USA Abstract Chondrichthyans are a class of fishes threatened with habitat destruction and fishing pressures. The current study presents the complete mitochondrial genome sequence (17,688 bp) of the vulnerable Hortle’s whipray, Himantura hortlei. The mitochondrial genome arrangement is consistent with that seen in most vertebrates, containing 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 control region. Phylogenetic analyses were performed based on mitogenome and ND2 sequences. Under our taxon sampling scheme, Himantura hortlei was found to be most closely related to H. fai. Keywords Chondrichthyes, long-PCR, Myliobatiformes, NGS, phylogeny History Received 23 February 2015 Accepted 14 March 2015 Published online 27 May 2015 Introduction The Hortle’s whipray, Himantura hortlei, is a moderately large viviparous ray distributed in the western Pacific. It lives in shallow water up to 10m in depth and is typically found in estuaries and intertidal mud flats where it feeds on crustaceans, mollusks, and small fishes (Last et al., 2006; White et al., 2009). This species is currently listed as vulnerable by the IUCN red list (White et al., 2009). It is threatened by habitat destruction and fishing pressure due to accidental bycatch. The mitogenome sequence of H. hortlei will provide a reference to aid in identification, management, and conservation of the species. In the present study, we describe the complete mitogenome sequence of H. hortlei and investigate its phylogenetic position relative to other stingrays. Materials and methods The Himantura hortlei specimen (CSIRO H 5977-01) used in this study was captured in Indonesia. The complete mitogenome sequence was determined through a long-PCR and next-gener- ation sequencing protocol (Yang & Naylor, 2014). The sequence was annotated using MitoAnnotator (Atmosphere and Ocean Research Institute, University of Tokyo, Japan) (Iwasaki et al., 2013). A total of 37 full mitogenome sequences were downloaded from GenBank (Figure 1). Their ND2 sequences were retrieved to make an alignment with the 10,991 sequences (as of 28 February 2015) from our ND2 database (Naylor et al., 2012b). A neighbor- Joining tree was then constructed under the uncorrected P distance using PAUP*4.0.b10 (Sinauer Associates, Sunderland, MA) (Swofford, 2002) to verify the species identification of these GenBank sequences. Species names were updated when neces- sary (Figure 1). Protein-coding gene sequences of the 37 mitogenomes and the newly acquired H. hortlei mitogenome were aligned. The complementary strand sequences were used for ND6. Incomplete stop codons of genes were excluded from the alignment. The length of the final alignment is 11,475 bp. The dataset was partitioned using PartitionFinder v1.1.1 (Lanfear et al., 2014) and subjected to maximum Likelihood analysis (100 runs) using RAxML v.8.0.26 (Stamatakis, 2014). The mitogen- ome alignment was augmented with 30 additional ND2 sequences derived from different species of Himantura and allies (Naylor et al., 2012a). This augmented dataset was subsequently subjected to constraint searches (100 runs) in which the original topology derived from the whole mitogenome analysis was held constant and the additional ND2 sequences were placed onto this framework. Bootstrap analyses (1000 replicates) were also performed using RAxML. Results and discussion The length of the H. hortlei mitogenome sequence (GenBank accession number: KP727646) was determined to be 17,688 bp, which included 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region typical of vertebrates. Twenty-nine of the 38 elements were encoded on the heavy strand. One protein-coding gene (ND6) and eight tRNA genes were encoded on the light strand. See GenBank for more detailed characteristics of this mitogenome. The likelihood score of the optimal tree (Figure 1) is 169,962.632465. The order Myliobatiformes was resolved as monophyletic. The species Urogymnus asperrimus is placed within the genus Himantura, consistent with the findings of Naylor et al. (2012a). In the current analysis, Himantura hortlei is found to be sister to H. fai (bootstrap value ¼ 98%). Correspondence: Hayley M. DeHart, Hollings Marine Laboratory, College of Charleston, 331 Fort Johnson Road, Charleston, SC 29412, USA. E-mail: townsendh@g.cofc.edu Mitochondrial DNA Downloaded from informahealthcare.com by University of New Hampshire on 05/28/15 For personal use only.