http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007312

MITOGENOME ANNOUNCEMENT

The complete mitogenome of the Australian freshwater shrimp Paratya australiensis Kemp, 1917 (Crustacea: Decapoda: Atyidae) Huan You Gan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University, Jalan Lagoon Selatan, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, Monash University, Jalan Lagoon Selatan, Selangor, Malaysia

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1

Abstract

Keywords

The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.

Atyoidea, mitochondria, molecular resources

Atyid shrimps are common inhabitants of freshwater environments in the tropics and many temperate regions. The superfamily Atyoidea is one of the largest within the infraorder Caridea and contains just the single family, the Atyidae (De Grave et al., 2009). The Atyidae is a large family with over 400 species placed in approximately 40 genera (De Grave et al., 2009); however, the classification of these shrimps at all taxonomic levels is in need of a substantial overhaul (von Rintelen et al., 2012). Paratya is a relatively speciose genus of atyid shrimps, with approximately 15 species distributed widely across the western pacific from Japan to southern Australia (Page et al., 2005). The taxonomy of Australia’s Paratya species has been controversial but the prevailing view until recently has been that of Williams & Smith (1979) who considered Paratya to be represented by a

History Received 23 December 2014 Accepted 30 December 2014 Published online 19 February 2015

single species, Paratya australiensis in Australia. Recent molecular studies have, however, revealed significant cryptic speciation throughout P. australiensis’s distribution (Cook et al., 2006; Page et al., 2005; Williams & Smith, 1979). To provide additional molecular resources for the study of the taxonomy and evolution of Paratya, and atyid shrimps more generally, the mitogenome sequence for P. australiensis is presented. This is the first Southern Hemisphere species of atyid shrimp to have its mitochondrial genome sequenced. The P. australiensis sample was caught with a hand-net from the Loddon River, Baringhup, Victoria. The purification of genomic DNA from ethanol-preserved abdominal muscle tissue, partial whole genome sequencing (2  250 bp paired-end run), mitogenome assembly and annotation were performed as

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

Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg)

Strand

Position

Length (bp)

H H H H H H H H H H H H

1–1542 1616–1679 1692–2399 2380–2447 2452–2520 2521–2679 2673–3347 3351–4136 4141–4205 4206–4559 4558–4621 4626–4688

1542 64 708 68 69 159 675 786 65 354 64 63

Inter-genic_ nucleotides (bp) 0 73 12 20 4 0 7 3 4 0 2 4

Start codon

Stop codon

ATT

TAA

ATG

TAA

Anticodon UAA UUU GUA

ATC ATG ATG

TAA TAA TAA

ATT

TAA

UAA UGC UCG (continued )

Correspondence: Han Ming Gan, School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia. E-mail: [email protected]

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H. Y. Gan et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Continued.

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Gene trnN(gtt) trnS1(tct) 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 trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta)

Strand

Position

Length (bp)

H H H L L L L L H L H H H L L L L L

4690–4754 4760–4827 4828–4896 4895–4959 4960–6690 6688–6751 6754–8091 8085–8381 8412–8477 8478–8544 8547–9062 9062–10,198 10,201–10,270 10,288–11,229 11,269–11,335 11,283–12,649 12,691–12,756 12,758–13,553 13,554–14,559 14,560–14,628 14,651–14,718 14,722–14,788 14,795–15,793 15,793–15,859 15,867–15,929 15,932–15,990

65 68 69 65 1731 64 1338 297 66 67 516 1137 70 942 67 1367 66 796 1006 69 68 67 999 67 63 59

H L H H H L L

previously described (Gan et al., 2014). A modification to the method in mitogenome assembly was to use the IDBA-UD program to de novo assemble the mitogenome (Peng et al., 2012). The P. australiensis mitochondrial genome is 15,990 bp in length (GenBank accession number: KM978917) and has 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 1006 bp (Table 1). The mitogenome base composition is 35.16% A, 33.55% T, 13.06% G and 18.24% C and the order of genes is identical to other Atyid species which share the same arrangement as species of Macrobrachium shrimps (Palaemonidae), which is consistent with the ancestral pan crustacean pattern (Miller et al., 2005). Our sample of P. australiensis shows a 99% similarity to a 635 bp fragment of the COI gene for a sample of P. australiensis from the study by Hurwood et al. (2003). It will be of interest to study additional complete mitogenome sequences to address the many taxonomic issues and evolutionary questions within the species, the genus and the family (Cook et al., 2006; Hurwood et al., 2003; Page et al., 2005; von Rintelen et al., 2012). It is also likely that mitogenome information in the form of gene order rearrangements will be useful for providing insights into relationships within the infraorder Caridea as certain lineages and groups show a number of rearrangements including the palaemonid Exopalaemon carinicauda (Shen et al., 2009) and alpheid (Alpheus) shrimps (Shen et al., 2012).

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 article.

References Cook BD, Baker AM, Page TJ, Grant SC, Fawcett JH, Hurwood DA, Hughes JM. (2006). Biogeographic history of an Australian freshwater

Inter-genic_ nucleotides (bp) 1 5 0 2 0 3 2 7 30 0 2 1 2 17 39 53 41 1 0 0 22 3 6 1 7 2

Start codon

Stop codon

Anticodon GUU UGU UUC GAA

ATA

TAA

ATG ATT

TAA TAA

GUG UGU UGG ATT ATG

TAA TAA

ATC

TAG

ATT

AAT

TAA

AAT

UGA UAG UAC GAU UUG CAU ATT

TAA UCA GCA GUA

shrimp, Paratya australiensis (Atyidae): The role life history transition in phylogeographic diversification. Mol Ecol 15:1083–93. De Grave S, Pentcheff ND, Ahyong ST, Chan TY, Crandall KA, Al E. (2009). A classification of living and fossil genera of decapod crustaceans. Raffles Bull Zool 1:1–109. 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. Hurwood DA, Hughes JM, Bunn SE, Cleary C. (2003). Population structure in the freshwater shrimp Paratya australiensis inferred from allozymes and mitochondrial DNA. Heredity (Edinb) 90: 64–70. Miller AD, Murphy NP, Burridge CP, Austin CM. (2005). Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol (NY) 7:339–49. Page TJ, Baker AM, Cook BD, Hughes JM. (2005). Historical transoceanic dispersal of a freshwater shrimp: The colonization of the South Pacific by the genus Paratya (Atyidae). J Biogeogr 32: 581–93. Peng Y, Leung HCM, Yiu SM, Chin FYL. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420–8. Shen X, Li X, Sha Z, Yan B, Xu Q. (2012). Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): Gene rearrangement and phylogeny within Caridea. Sci China Life Sci 55:591–8. Shen X, Sun M, Wu Z, Tian M, Cheng H, Zhao F, Meng X. (2009). The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes. Gene 437:1–8. Von Rintelen K, Page TJ, Cai Y, Roe K, Stelbrink B, Kuhajda BR, Iliffe TM, et al. (2012). Drawn to the dark side: A molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses. Mol Phylogenet Evol 63:82–96. Williams WD, Smith MJ. (1979). A taxonomics revision of Australian species of Paratya (Crustacea: Atyidae). Austral J Marine Freshwater Res 30:815–32.

The complete mitogenome of the Australian freshwater shrimp Paratya australiensis Kemp, 1917 (Crustacea: Decapoda: Atyidae).

The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the supe...
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