http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971305 MITOGENOME ANNOUNCEMENTS Novel gene arrangement in the mitochondrial genome of the Corte ´s Geoduck clam (Panopea globosa) Celia Isabel Bisbal-Pardo 1 , Miguel Angel del Rı ´o-Portilla 2 , and Axaya ´catl Rocha-Olivares 1 1 Molecular Ecology Laboratory, Biological Oceanography Department, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California, Me ´xico and, 2 Aquaculture Department, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California, Me ´xico Abstract The mitogenome of the Corte ´s geoduck clam Panopea globosa (Genbank accession KM580068) has a length of 15,469 bp and contains 13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNA genes, as conventional metazoan mitochondrial genomes. Structural genes start with ATG, ATA and GTG codons; whereas TAG and TAA are used as stop codons. Base composition is: 23.3% A, 40.4% T, 10.1% C and 26.1% G. As is typical of marine bivalves, all genes are coded on the same strand. On the other hand, the gene arrangement is considerably different from those found in other heterodont bivalve mitogenomes. Keywords Bivalve, heterodont, mitogenome, Panopea globosa History Received 24 September 2014 Accepted 26 September 2014 Published online 20 October 2014 The Corte ´s Geoduck, Panopea globosa (Dall, 1898), is a marine bivalve endemic of the Northwest Mexican coast. Its common name refers to its first known distribution: the Sea of Corte ´s [SC], but its geographic range has been recently extended to the Pacific coast [PC] of Baja California Sur [BCS] (Sua ´rez-Moo et al., 2013). The Corte ´s Geoduck and its congener the Pacific Geoduck, P. generosa, sustain highly valued fisheries in Mexico (Arago ´n- Noriega et al., 2012). The complete mitochondrial DNA of P. globosa was obtained from two organisms from San Felipe (upper Gulf of California) and one from Bahı ´a Magdalena (Pacific coast of BCS). Genomic DNA was extracted from siphon tissue with the DNeasy blood and tissue kit (QIAGEN, Hilden, Germany). Separate DNA libraries (500 bp insert) were constructed with the TruSeq NanoÔ kit (Illumina, San Diego, CA) and each sequenced using 1/12 of a single lane (100 pb paired ends) of a HiSeq 2500 ultra-high- throughput sequencer (Illumina, San Diego, CA), at the Laboratorio Nacional de Geno ´mica para la Biodiversidad (LANGEBIO, Irapuato, Mexico). All reads passed a quality control with Fast QC v 0.10.1 (Babraham Institute, Cambridge, UK) (Andrews, 2011); additional QC and trimming was imple- mented in CLC Genomics Workbench 7.0.3 (CLC bio, Boston, MA), which was also used for de novo assembly. Gene annotation was carried using MITOS (Bernt et al., 2013) and BLAST searches. Boundaries of structural and rRNA genes were resolved using other available bivalve mitochondrial sequences. The tRNA genes were identified by DOGMA (Wyman et al., 2004), MITOS and t-RNA scan-SE Search Server (Lowe & Eddy, 1997). The Panopea globosa mitogenome (Genbank accession KM580068) is 15,469 bp in size with a base composition of: A 23.3%, T 40.4%, C 10.1% and G 26.1%. It encodes in the same DNA strand 13 proteins, two ribosomal RNA and 22 transfer RNA genes (Figure 1). Most structural genes start with the conventional codons (eight with ATG and three with ATA), only CoxI and Cytb start with an alternative codon (GTG). Eight genes are terminated by TAG and five by TAA. A total of 789bp non- coding nucleotides are spread among intergenic regions than range from one to 316 bp. The longest non-coding region is located between CoxI and CoxII, similar to its congener P. generosa in which it is 122 bp longer. The gene arrangement of Corte ´s geoduck mitogenome is identical to that of P. generosa (Bisbal-Pardo et al., 2014), but they differ substantially from those of other known heterodont bivalves (Dreyer & Steiner, 2006, Yuan et al., 2012) (Figure 1). The genome wide divergence between allopatric SC and PC clams was 0.25%. This genome increases the number of completely sequenced mitogenomes within the subclass Heterodonta and will be useful for phylogen- etic studies. Correspondence: Axaya ´catl Rocha-Olivares, Molecular Ecology Laboratory, Biological Oceanography Department, Centro de Investigacio ´n Cientı ´fica y de Educacio ´n Superior de Ensenada, B.C. (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California, Me ´xico. Tel: +52(646)1750500. E-mail: arocha@cicese.mx Mitochondrial DNA Downloaded from informahealthcare.com by 158.97.12.238 on 10/20/14 For personal use only.