http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.900611 MITOGENOME ANNOUNCEMENT The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing Nick A. Robinson 1,2 , Nathan E. Hall 3,4 , Elizabeth M. Ross 5 , Ira R. Cooke 4,6 , Brett P. Shiel 3 , Andrew J. Robinson 4,6 , and Jan M. Strugnell 3 1 Department of Breeding and Genetics, Nofima, A ˚ s, Norway, 2 Department of Biological Sciences, Flinders University, Bedford Park, South Australia, Australia, 3 Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia, 4 Life Sciences Computation Initiative, VLSCI, The University of Melbourne, Melbourne, Victoria, Australia, 5 Department of Environment and Primary Industries, BioSciences Research, Bundoora, Victoria, Australia, and 6 Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia Abstract The mitochondrial genome of greenlip abalone, Haliotis laevigata, is reported. MiSeq and HiSeq sequencing of one individual was assembled to yield a single 16,545 bp contig. The sequence shares 92% identity to the H. rubra mitochondrial genome (a closely related species that hybridize with H. laevigata in the wild). The sequence will be useful for determining the maternal contribution to hybrid populations, for investigating population structure and stock- enhancement effectiveness. Keywords Complete mitochondrial genome, greenlip abalone, Haliotis laevigata, massive parallel sequencing History Received 23 February 2014 Accepted 1 March 2014 Published online 24 March 2014 Greenlip abalone, Haliotis laevigata, is distributed along the western and southern coastlines of mainland Australia and northern Tasmania. Fisheries and aquaculture of the species is of high commercial value. Blacklip abalone, H. rubra, has an overlapping range and is known to hybridize with H. laevigata (Brown, 1995). Hybrids are preferred by some farmers. Fishery stock enhancement has been recently considered for parts of the H. laevigata fishery (Hart et al., 2013a,b,c). Analysis of mitochondrial genome variation can be used to study stock structure and hybridization, and can provide useful information with implications for the management of the fishery. One adult H. laevigata was collected from the coast of Australia (38  28 0 S,145  2 0 E), dissected and frozen at 80  C. Whole genomic DNA was extracted from the epipodial tentacle tissue. Two DNA libraries were prepared for Illumina massive parallel sequencing. The libraries were sequenced on the MiSeq and HiSeq (Illumina) producing a total 22.9 Gbp of data. Adapter contamination, PCR duplicates, short and low quality average reads and ends were removed. After quality control 19.7 Gbp (85.9%) of sequence was used for subsequent analysis. De novo assembly was performed using Gossamer (Conway et al., 2012). Protein coding regions and ribosomal sequences were determined using MITOS (Bernt et al., 2013). The individual sequenced was homoplasmic (no SNPs were detected). The mitDNA sequence was 16,545 bp long, with average sequence depth of 200, with 22 tRNAs, 2 rRNAs and 13 protein coding sequences (GenBank KJ472483: Table 1). Nucleotide composition was 57.8% AT. Most coding sequences were initiated with an AT[G/C] codon, the exceptions being nad1 (GTG), nad4 (GGG) and cox2 (TTG). All protein coding sequences terminated with a conventional stop codon (TAA or TAG, Table 1). Haliotis laevigata and H. rubra (AY588938.1, Maynard et al., 2005) share 92% nucleotide sequence identity with 43 aa differences across 12 of 13 proteins (Table 1). Base differences are evenly spread over the genome except in two areas, one non- coding stretch of 5 bases (GATAA) between the tRNA Cys and tRNA Tyr present in H. laevigata but not H. rubra, and one stretch of 25 bases in the 12S rRNA gene (CTGTATTTGTTATACGGA TTTTTCCC) present in H. rubra but not H. laevigata. A 21bp part of this latter stretch of sequence (TATTTGTTATACGGATT TTTC) is identical to a preceding stretch found in both species and appears to be repeated in tandem in H. rubra but not H. laevigata. Repetition could not be detected in other abalone 12S rRNA sequences (DQ279804.1; H. laevigata, DQ276985.1; H. roei). Correspondence: Nick A. Robinson, Department of Breeding and Genetics, Nofima, P.O. Box 210, N-1431 A ˚ s, Norway. Tel: +61 448984002. E-mail: nick.robinson@nofima.no Mitochondrial DNA Downloaded from informahealthcare.com by Matforsk on 03/25/14 For personal use only.