Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae) 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 moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945572
Published online: 04 Aug 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 06 November 2015, At: 02:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945572
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae) 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 [University of California, San Diego] at 02:26 06 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
Matutidae, mitogenome, molecular resource
The crab family Matutidae contains a distinctive group of predatory crabs with adaptions for swimming or digging. Often referred to as moon crabs, some 15 species placed in 4 genera are recognized from the family (Davie, 2014a, 2014b; De Grave et al., 2009; Ng et al., 2008). Members of the family have a distinctive flattened dactyl on each of their walking legs, which are used for swimming and digging into soft sediments. The taxonomy of the superfamily Calappoidea, containing the families Matutidae and Calappidae, is contentious (Ng et al., 2008). As this is the first mitogenome sequenced for the superfamily, we expect that this mitochondrial sequence will support taxonomic and evolutionary research on these interesting but relatively poorly studied crabs. A specimen of Ashtoret lunaris was obtained from the intertidal zone at Casuarina beach, Darwin, Northern Territory. The purification of genomic DNA from the claw muscle tissue,
History Received 9 July 2014 Accepted 13 July 2014 Published online 4 August 2014
partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Bernt et al., 2012; Gan et al., 2014; Hahn et al., 2013). The partial 16S ribosomal RNA gene sequence from an isolate of Ocypode quadrata (GenBank accession number: FN539018) was used as the initial bait for MITObim assembly. The complete mitogenome of A. lunaris was 15,807 bp in length (GenBank accession number: LK391941) and contains 37 mitochondrial genes and a non-coding AT-rich region of 956 bp in length (Table 1). The mitogenome gene order was typical for brachyuran crabs (Miller et al., 2005). The A. lunaris mitogenome base composition was 35% A, 35% T, 11% G and 19% C and was most similar (76.0%) in terms of the entire mitogenome to Pseudocarcinus gigas (Family Menippidae) based on discontinuous MegaBLAST (Miller et al., 2005). Our sample showed 92%
Table 1. Annotation of the complete mitochondrial genome of A. lunaris. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt)
Strand
Position
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
H H H H H H H H H H H H H
1–1539 1535–1600 1608–2315 2296–2363 2366–2428 2429–2587 2581–3255 3259–4048 4049–4113 4111–4467 4466–4531 4532–4597 4600–4667
1539 66 708 68 63 159 675 790 65 357 66 66 68
0 5 7 20 2 0 7 3 0 3 2 0 2
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
ATG ATT ATG
TAA TAA T
ATA
TAA
UCC UGC UCG GUU (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]
2
M. H. Tan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 02:26 06 November 2015
Gene trnS1(tct) trnE(ttc) trnH(gtg) trnF(gaa) nad5 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)
Intergenic nucleotides
H H L L L L L H L H H H L L L L L – H L H H H L L
4675–4741 4742–4808 4808–4869 4870–4933 4970–6665 6704–8044 8038–8340 8343–8408 8409–8475 8478–8987 8987–10,121 10,122–10,189 10,203–11,150 11,173–11,241 11,196–12,567 12,549–12,621 12,620–13,439 13,440–14,395 14,396–14,461 14,459–14,526 14,529–14,599 14,600–15,610 15,609–15,675 15,675–15,741 15,743–15,807
67 67 62 64 1696 1341 303 66 67 510 1135 68 948 69 1372 73 820 956 66 68 71 1011 67 67 65
7 0 1 0 36 38 7 2 0 2 1 0 13 22 46 19 2 0 0 3 2 0 2 1 1
similarity to a specimen of A. lunaris sequenced for a 680 bp fragment of the COI gene (HM180672) in the study by Kim et al. (2012) which was based on a sample collected from South Korea identified using BLAST. Our sample was 97% similarity to a sample sequenced from Queensland Australia on the BOLD data base (http://www.boldsystems.org) for a 604 bp COI fragment. However, tree-based identification on BOLD indicates there are significant taxonomic issues that need to be addressed with respect to morphological identifications and/or the delineation of species boundaries in Ashtoret (data can be provided upon request).
Acknowledgements We are grateful to Professor Peter Ng Kee Lin, National University of Singapore for providing taxonomic advice.
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 Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo
Start codon
Stop codon
Anticodon UCU UUC GUG GAA
ATG ATG ATG
T TAA TAA UGU UGG
ATG ATG
TAA T
GTG
TAA
UGA UAG UAC GAT UUG CAU ATG
TAA UCA GCA GUA
metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6. Davie P. (2014a). Matutidae De Haan, 1835 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼106759 (Accessed 23 June 2014). Davie P. (2014b). Thalamita Latreille, 1892. World Register of Marine Species, 2014. Available at: http://www.marinespecies.org/ aphia.php?p=taxdetails&id=106931 (Accessed 23 Jun 2014). De Grave S, Pentcheff ND, Ahyong ST, Chan TY, Crandall KA, Dworschak PC, Felder DL, et al. (2009). A classification of living and fossil genera of decapod Crustaceans. Raff Bull Zool 21:1–109. 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. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41: e129. Kim D-W, Yoo WG, Park HC, Yoo HS, Kang DW, Jin SD, Min HK, et al. (2012). DNA barcoding of fish, insects, and shellfish in Korea. Genomics Inform 10:206–11. Miller A, Murphy N, Burridge C, Austin C. (2005). Complete mitochondrial DNA sequences of the decapod Crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7:339–49. Ng PKL, Guinot D, Davie P. (2008). Systema Brachyurorum: Part 1. An annotated checklist of extant brachyuran crabs of the world. Raff Bull Zool 17:1–286.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae) 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 moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945572
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 15
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 06 November 2015, At: 02:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945572
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae) 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 [University of California, San Diego] at 02:26 06 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.
Matutidae, mitogenome, molecular resource
The crab family Matutidae contains a distinctive group of predatory crabs with adaptions for swimming or digging. Often referred to as moon crabs, some 15 species placed in 4 genera are recognized from the family (Davie, 2014a, 2014b; De Grave et al., 2009; Ng et al., 2008). Members of the family have a distinctive flattened dactyl on each of their walking legs, which are used for swimming and digging into soft sediments. The taxonomy of the superfamily Calappoidea, containing the families Matutidae and Calappidae, is contentious (Ng et al., 2008). As this is the first mitogenome sequenced for the superfamily, we expect that this mitochondrial sequence will support taxonomic and evolutionary research on these interesting but relatively poorly studied crabs. A specimen of Ashtoret lunaris was obtained from the intertidal zone at Casuarina beach, Darwin, Northern Territory. The purification of genomic DNA from the claw muscle tissue,
History Received 9 July 2014 Accepted 13 July 2014 Published online 4 August 2014
partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Bernt et al., 2012; Gan et al., 2014; Hahn et al., 2013). The partial 16S ribosomal RNA gene sequence from an isolate of Ocypode quadrata (GenBank accession number: FN539018) was used as the initial bait for MITObim assembly. The complete mitogenome of A. lunaris was 15,807 bp in length (GenBank accession number: LK391941) and contains 37 mitochondrial genes and a non-coding AT-rich region of 956 bp in length (Table 1). The mitogenome gene order was typical for brachyuran crabs (Miller et al., 2005). The A. lunaris mitogenome base composition was 35% A, 35% T, 11% G and 19% C and was most similar (76.0%) in terms of the entire mitogenome to Pseudocarcinus gigas (Family Menippidae) based on discontinuous MegaBLAST (Miller et al., 2005). Our sample showed 92%
Table 1. Annotation of the complete mitochondrial genome of A. lunaris. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt)
Strand
Position
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
H H H H H H H H H H H H H
1–1539 1535–1600 1608–2315 2296–2363 2366–2428 2429–2587 2581–3255 3259–4048 4049–4113 4111–4467 4466–4531 4532–4597 4600–4667
1539 66 708 68 63 159 675 790 65 357 66 66 68
0 5 7 20 2 0 7 3 0 3 2 0 2
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
ATG ATT ATG
TAA TAA T
ATA
TAA
UCC UGC UCG GUU (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]
2
M. H. Tan et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Downloaded by [University of California, San Diego] at 02:26 06 November 2015
Gene trnS1(tct) trnE(ttc) trnH(gtg) trnF(gaa) nad5 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)
Intergenic nucleotides
H H L L L L L H L H H H L L L L L – H L H H H L L
4675–4741 4742–4808 4808–4869 4870–4933 4970–6665 6704–8044 8038–8340 8343–8408 8409–8475 8478–8987 8987–10,121 10,122–10,189 10,203–11,150 11,173–11,241 11,196–12,567 12,549–12,621 12,620–13,439 13,440–14,395 14,396–14,461 14,459–14,526 14,529–14,599 14,600–15,610 15,609–15,675 15,675–15,741 15,743–15,807
67 67 62 64 1696 1341 303 66 67 510 1135 68 948 69 1372 73 820 956 66 68 71 1011 67 67 65
7 0 1 0 36 38 7 2 0 2 1 0 13 22 46 19 2 0 0 3 2 0 2 1 1
similarity to a specimen of A. lunaris sequenced for a 680 bp fragment of the COI gene (HM180672) in the study by Kim et al. (2012) which was based on a sample collected from South Korea identified using BLAST. Our sample was 97% similarity to a sample sequenced from Queensland Australia on the BOLD data base (http://www.boldsystems.org) for a 604 bp COI fragment. However, tree-based identification on BOLD indicates there are significant taxonomic issues that need to be addressed with respect to morphological identifications and/or the delineation of species boundaries in Ashtoret (data can be provided upon request).
Acknowledgements We are grateful to Professor Peter Ng Kee Lin, National University of Singapore for providing taxonomic advice.
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 Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo
Start codon
Stop codon
Anticodon UCU UUC GUG GAA
ATG ATG ATG
T TAA TAA UGU UGG
ATG ATG
TAA T
GTG
TAA
UGA UAG UAC GAT UUG CAU ATG
TAA UCA GCA GUA
metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6. Davie P. (2014a). Matutidae De Haan, 1835 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼106759 (Accessed 23 June 2014). Davie P. (2014b). Thalamita Latreille, 1892. World Register of Marine Species, 2014. Available at: http://www.marinespecies.org/ aphia.php?p=taxdetails&id=106931 (Accessed 23 Jun 2014). De Grave S, Pentcheff ND, Ahyong ST, Chan TY, Crandall KA, Dworschak PC, Felder DL, et al. (2009). A classification of living and fossil genera of decapod Crustaceans. Raff Bull Zool 21:1–109. 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. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41: e129. Kim D-W, Yoo WG, Park HC, Yoo HS, Kang DW, Jin SD, Min HK, et al. (2012). DNA barcoding of fish, insects, and shellfish in Korea. Genomics Inform 10:206–11. Miller A, Murphy N, Burridge C, Austin C. (2005). Complete mitochondrial DNA sequences of the decapod Crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7:339–49. Ng PKL, Guinot D, Davie P. (2008). Systema Brachyurorum: Part 1. An annotated checklist of extant brachyuran crabs of the world. Raff Bull Zool 17:1–286.
