Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis

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The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura) Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin To cite this article: Mun Hua Tan, Han Ming Gan, Yin Peng Lee & Christopher M. Austin (2014): The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.989515

Published online: 26 Dec 2014.

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Date: 07 November 2015, At: 14:43

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.989515

MITOGENOME ANNOUNCEMENT

The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia

Downloaded by [Australian National University] at 14:43 07 November 2015

1

Abstract

Keywords

The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp consisting of 13 proteincoding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.

Anomura, Galatheoidea, mitogenome, porcellanid crab

Porcellanid crabs are placed in the family Porcellanidae, one of four extant families recognized within the superfamily Galatheoidea, which in turn is one of the seven extant superfamilies within the infraorder Anomura (Ahyong et al., 2010). The Anomura itself is highly diverse with over 2500 species and represents an extraordinary range of body forms and species that have adapted to a wide range of habitats in freshwater, terrestrial and hydrothermal vent ecosystems (Bracken-Grissom et al., 2013). The Porcellanidae is one of the most diverse families within the Galatheoidea, with over 250 species placed in 30 genera (Osawa & McLaughlin, 2010; WORMS, 2014). These crabs superficially resemble true crabs and have flattened bodies adapted to living in crevices and under rocks. Petrolisthes is a diverse genus with over 100 recognized species, with a global distribution including both tropical and temperate regions (Osawa, 2014). They are considered useful crustacean models for studies of environmental and thermal adaptation (Tagmount et al., 2010) and of importance to phylogenetic understanding of diversification of the Anomura (Bracken-Grissom et al., 2013). Relatively little genomic and molecular genetic information is available for this family, which is true of the Anomura more generally. Mitogenome resources for the Anomura is limited to only five mitogenomes as recorded on GenBank (Shen et al., 2013). Petrolisthes haswelli is a little-studied species, occurring across northern Australia where it is possibly endemic

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

History Received 16 November 2014 Accepted 16 November 2014 Published online 26 December 2014

(Haig, 1965). We have sequenced the mitogenome of P. haswelli to provide additional molecular resources for the study of the taxonomy and phylogeny of porcellanid crabs and the Anomura more widely. The P. haswelli sample was caught from under rocks on the Nightcliff beach intertidal zone, Darwin, Northern Territory. A voucher specimen has been lodged with the he Museum and Art Gallery of the Northern Territory (Registration Number: Cr018575). The purification of genomic DNA from ethanol-preserved leg muscle tissue, partial whole genome sequencing (2  150 bp paired-end run) were performed as previously described (Gan et al., 2014). Genome assembly was carried out using IDBA-UD, (Peng et al., 2012), which led to the recovery of the complete mitogenome as the longest contig in the assembly. Subsequent re-circularization and annotation of the mitogenome were done as previously described by Gan et al. (2014). The P. haswelli mitochondrial genome is 15,348 bp in length (GenBank accession number: LN624374) and has 37 mitochondrial genes (13 protein-coding genes, two rRNAs and 22 tRNAs) and a non-coding region of 603 bp (Table 1), with a base composition of 34% A, 36% T, 11% G and 19% C. The order of genes is identical to Neopetrolisthes maculatus, the only other porcellanid crab with a complete mitogenome sequence, but differs from the mitogenome of the hydrothermal vent crab, Shinkaia crosnieri, from the related family Galatheidae. Our sample of P. haswelli shows the highest similarity (88.4%) to a 544 bp 16S ribosomal RNA gene fragment from the west Atlantic species Petrolisthes rosariensis (GenBank accession number: DQ865305) (Hiller et al., 2006; Rodrı´guez et al., 2006). This mitogenome will be a valuable resource for taxonomic and phylogenetic investigations of the family, superfamily (Hiller et al., 2006; Rodrı´guez et al., 2006) and Anomura more widely (Bracken-Grissom et al., 2013; Shen et al., 2013).

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M. H. Tan et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Annotation of the complete mitochondrial genome of Petrolisthes haswelli.

Downloaded by [Australian National University] at 14:43 07 November 2015

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

Strand

Position

Length (bp)

Intergenic nucleotides

Start codon

Stop codon

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

1–1539 1535–1600 1605–2289 2290–2353 2358–2422 2423–2773 2772–2834 2840–2903 2904–2969 2970–3950 3949–4013 4014–4172 4166–4840 4844–5635 5640–5703 5703–5768 5769–5833 5834–5899 5900–5965 5967–7691 7689–7754 7755–9090 9084–9386 9389–9453 9476–9988 9988–11,122 11,123–11,190 11,194–11,259 11,263–12,189 12,222–12,287 12,246–13,615 13,602–13,675 13,675–14,463 14,464–15,066 15,067–15,134 15,154–15,220 15,221–15,283 15,284–15,347

1539 66 685 64 65 351 63 64 66 981 65 159 675 792 64 66 65 66 66 1725 66 1336 303 65 513 1135 68 66 927 66 1370 74 789 603 68 67 63 64

1 5 4 0 4 0 2 5 0 0 2 0 7 3 4 1 0 0 0 1 3 0 7 2 22 1 0 3 3 32 42 14 1 0 0 19 0 0

ACG

TAA

ATG

T

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.

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Anticodon UAA UUU UCC

ATT

TAA UGC GAU CAU

ATT

TAA

GTG ATG ATG

TAA TAA TAG

GUC

UCG GUU UCU UUC GAA ATC

TAA

ATG ATG

T TAA

ATT ATG

TAA T

GUG UGU UGA ATA

TAG UAG UAC UCA UUG GCA GUA

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