http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.974173

MITOGENOME ANNOUCEMENT

The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca) Han Ming Gan1,2, Mun Hua Tan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2

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1

School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Selangor, Malaysia Abstract

Keywords

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 proteincoding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.

Branchiopoda, mitogenome, tadpole shrimp

The Branchiopoda is a diverse crustacean group with over 1000 species that includes species that can be considered living fossils with morphologies that resemble fossil forms from the Cambrian and Devonian periods (Korn et al., 2013; Richter et al., 2007; Umetsu et al., 2002). While the group has been subject to a number of morphological and molecular-based studies there has been disputation regarding the higher level classification (Korn et al., 2013; Richter et al., 2007). The taxonomic treatment of several branchiopod groups has been varied and subject to both taxonomic splitting and lumping, however it is becoming apparent that a number of lineages are subject to cryptic speciation (Korn et al., 2013; Vanschoenwinkel et al., 2012). There has been significant systematic interest in tadpoles shrimps, placed in the genus Triops within the Notostraca, which has a global distribution and is now thought to comprise approximately 10 species (Korn et al., 2013). While 2 mitogenomes for Triops species are available and 7 for Branchiopoda more generally, no species from Australia have been sequenced for their complete mitogenome. We therefore present the full mitogenome of Triops australiensis from central Australia as a resource to support further phylogenetic and molecular taxonomic studies of this ancient group. This species has an extensive distribution across Australia where it is commonly found in ephemeral pools of water in arid regions (Tyler et al., 1996; Williams, 1968). A sample of T. australiensis was collected south of Alice Springs, Northern Territory, Australia by S. Williamson. The purification of genomic DNA from ethanol-preserved abdominal

History Received 3 October 2014 Accepted 5 October 2014 Published online 20 October 2014

tissue, partial whole genome sequencing (2  150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014) with one modification e.g. NEXTflex Rapid Illumina DNA library prep kit (Bioo Scientific, Austin, TX) was used in place of Nextera (Illumina, San Diego, CA) to prepare the sequencing library. The cox1 gene sequence of Triops australiensis isolate AUS_U_2 (GenBank accession number: JN175245) was used as the initial bait for MITObim assembly. The T. australiensis mitochondrial genome is 15,125 bp in length (GenBank accession number: NC_024439) and has 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 468 bp (Table 1). The base composition is 36.4% A, 16.1% C, 12.3% G and 35.1% T– – and the order of genes is identical to other Triops species and matches the conserved pancrustacean mitogenome order (Cook et al., 2005; Umetsu et al., 2002). The complete T. australiensis mitogenome sequence is closer to T. longicaudatus (84.9% similariry) than to T. cancriformis (78.3% similarity) consistent with phylogenetic studies (Korn et al 2013). Our sample of T. australiensis is 97.6% similar for a 509 fragment of the 16S rRNA region from an animal sampled from the Paroo area, NSW, Australia (ZMUC CRU-9940) (GenBank accession number: EF189616.1) studied by Korn et al. (2013). We look forward to further studies utilising this and other Branchiopod mitogenomes to further the understanding of speciation and evolution in this ancient lineage.

Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Malaysia. E-mail: [email protected]

2

H. M. Gan et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Annotation of the complete mitochondrial genome of T. australiensis.

Mitochondrial DNA Downloaded from informahealthcare.com by Mcgill University on 11/03/14 For personal use only.

Gene trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta) cox1 trnL2(taa) cox2 trnK(ctt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(gct) trnE(ttc) trnF(gaa) nad5 trnH(gtg) nad4 nad4l trnT(tgt) trnP(tgg) nad6 cob trnS2(tga) nad1 trnL1(tag) rrnL trnV(tac) rrnS Control region

Strand

Position

Length (bp)

Intergenic nucleotides

H L H H H L L H H H H H H H H H H H H H H H L L L L L H L H H H L L L L L –

1–65 63–131 128–192 193–1185 1193–1258 1251–1312 1313–1376 1375–2913 2909–2976 2982–3662 3664–3733 3735–3798 3808–3957 3951–4622 4622–5410 5411–5473 5483–5827 5826–5889 5907–5969 5971–6041 6042–6106 6108–6173 6175–6240 6240–7958 7968–8031 8002–9352 9346–9663 9671–9735 9736–9799 9,803–10,300 10,300–11,433 11,437–11,506 11,524–12,435 12,452–12,516 12,477–13,859 13,824–13,894 13,894–14,657 14,658–15,125

65 69 65 993 66 62 64 1539 68 681 70 64 150 672 789 63 345 64 63 71 65 66 66 1719 64 1351 318 65 64 498 1134 70 912 65 1383 71 764 468

0 –3 –4 0 7 –8 0 –2 –5 5 1 1 9 –7 –1 0 9 –2 17 1 0 1 1 –1 9 –30 –7 7 0 3 –1 3 17 16 –40 –36 –1 0

Declaration of interest Funding for this study was provided by the Monash University Malaysia Tropical Medicine and Biology Multidisciplinary Platform. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

References Cook CE, Yue Q, Akam M. (2005). Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc Biol Sci 272: 1295–04. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Korn M, Rabet N, Ghate HV, Marrone F, Hundsdoerfer AK. (2013). Molecular phylogeny of the Notostraca. Mol Phylogenet Evol 69: 1159–71.

Start codon

Stop codon

Anticodon GAU UUG CAU

ATT

TAA UCA GCA GUA

TTG

TAA

ATG

TAA

UAA CUU GUC ATA ATG ATG

TAA TAA TAA

ATA

TAG

UCC UGC UCG GUU GCU UUC GAA ATT

TAG

ATG ATG

T– – TAA

GUG UGU UGG ATG ATG

TAA TAA

GTG

TAA

UGA UAG UAC

Richter S, Olesen J, Wheeler WC. (2007). Phylogeny of Branchiopoda (Crustacea) based on a combined analysis of morphological data and six molecular loci. Cladistics 23: 301–36. Tyler M, Davies M, Watson G, Williams D. (1996). Significant extension in northern Australia of the known geographic range of the Shield Shrimp Triops australiensis (Crustacea: Notostraca). Hydrobiologia 318:135–7. Umetsu K, Iwabuchi N, Yuasa I, Saitou N, Clark PF, Boxshall G, Osawa M, Igarashi K. (2002). Complete mitochondrial DNA sequence of a tadpole shrimp (Triops cancriformis) and analysis of museum samples. Electrophoresis 23:4080–4. Vanschoenwinkel B, Pinceel T, Vanhove MP, Denis C, Jocque M, Timms BV, Brendonck L. (2012). Toward a global phylogeny of the ‘‘living fossil’’ crustacean order of the Notostraca. PLoS One 7: e34998. Williams WD. (1968). The distribution of Triops and Lepidurus (Branchiopoda) in Australia. Crustaceana 14:119–26.

The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca).

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compar...
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