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 swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae) 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 swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945553
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: [Deakin University Library]
Date: 05 November 2015, At: 14:04
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945553
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the swimming crab Thalamita crenata (Ru¨ppell, 1830) (Crustacea; Decapoda; Portunidae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and 2School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Downloaded by [Deakin University Library] at 14:04 05 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of the swimming crab Thalamita crenata was obtained from a partial genome scan using the MiSeq sequencing system. The Thalamita crenata mitogenome has 15,787 base pairs (70% A+T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 897 bp non-coding AT-rich region. This Thalamita mitogenome sequence is the first for the genus and the eighth for the family Portunidae.
Molecular resource, mitogenome, Portunidae
The family Portunidae is a conspicuous and diverse group of crabs that contains a number of well-known shoreline and commercial species including the European shore crab, Carcinus maenas, mud crabs (Scylla) and swimming crabs (Portunus). More than 300 species placed in over 20 genera are recognized from the family (De Grave et al., 2009; Ng et al., 2008). Members of the family have a distinctive flattened dactyl on the fifth leg used for swimming. The taxonomy of the crabs included in the superfamily Portunoidea is contentious at both the family and subfamily levels (Schubart & Reuschel, 2009). We add another mitogenome to those available for the superfamily (8) by providing the first mitogenome for the genus Thalamita. This is the most diverse genus in the family after Portunus (Davie, 2014) and T. crenata, known as the mangrove swimming or spiny rock crab, is a familiar and wide spread species. It inhabits shallow and coastal waters throughout the Indo-Pacific exploiting both soft and hard substrates, where it can be subjected to local fishing pressure (Ng, 1998). We hope these mitochondrial sequences will stimulate evolutionary and population genetic research on these interesting but poorly studied crustaceans and anticipate they will be valuable for addressing taxonomic issues within the superfamily and the genus. An individual of T. crenata was collected from under rocks on the Nightcliff foreshore, Darwin, Northern Territory. The purification of genomic DNA from claw muscle tissue, partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 gene sequence of T. crenata (GenBank accession number: JX398104) was used as the initial bait for MITObim assembly. The complete mitogenome of T. crenata was 15,787 bp in length (GenBank accession number: LK391945) and contains 37 mitochondrial genes and a non-coding AT-rich region of 897 bp in length (Table 1). The mitogenome gene order is typical for brachyuran crabs and is identical to Portunus trituberculatus. The
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 26 June 2014 Accepted 27 June 2014 Published online 4 August 2014
T. crenata mitogenome base composition was 34% A, 35% T, 12% G and 19% C and is most similar in terms of the entire mitogenome to Charbydis japonicus (83.0%) consistent with the current subfamily classification. This is the eighth mitogenome for the Table 1. Annotation of the complete mitochondrial genome of T. crenata. Gene trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta) cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) 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
Strand
Position
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 –
1–66 64–132 136–205 206–1213 1212–1279 1279–1342 1343–1408 1409–2947 2943–3009 3025–3729 3710–3777 3778–3844 3845–4006 4003–4677 4677–5468 5468–5531 5529–5885 5889–5952 5956–6020 6021–6086 6089–6155 6156–6224 6244–6308 6312–6377 6377–8104 8125–9459 9453–9755 9758–9823 9824–9889 9892–10,398 10,398–11,532 11,533–11,598 11,628–12,584 12,590–12,658 12,615–13,973 13,981–14,054 14,057–14,890 14,891–15,787
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 66 69 70 1008 68 64 66 1539 67 705 68 67 162 675 792 64 357 64 65 66 67 69 65 66 1728 1335 303 66 66 507 1135 66 957 69 1359 74 834 897
0 3 3 0 2 1 0 0 5 15 20 0 0 4 1 1 3 3 3 0 2 0 19 3 1 20 7 2 0 2 1 0 29 5 44 7 2 0
GAU UUG CAU ATG
TAG UCA GCA GUA
ATG
TAA
ATG
TAA
UAA UUU GUC ATG ATA ATG
TAG TAA TAA
ATA
TAA
UCC UGC UCG GUU UCU UUC GUG GAA ATG ATG ATG
TAA TAG TAA UGU UGG
ATG ATG
TAA T
ATT
TAG
UGA UAG UAC
2
M. H. Tan et al.
family Portunidae, although four of these are from one genus (Scylla). Our sample is identical to a specimen of T. crenata sequenced for a 527 bp fragment of the cox1 gene (JX398104; Spiridonov et al., 2014). Comparison with the cox1 sequences on the BOLD, however suggests there are major taxonomic issues that need to be addressed at the species and generic levels as samples labeled as T. crenata show very high levels of intra-specific divergences (data can be provided upon request).
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.
Downloaded by [Deakin University Library] at 14:04 05 November 2015
References Davie P. (2014). Thalamita Latreille, 1892 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼106931 (Accessed 06 December 2014).
Mitochondrial DNA, Early Online: 1–2
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. 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. Ng PKL. (1998). Crabs. In: Carpenter KE, Niem VH, editors. The living marine resources of the Western Central Pacific. Vol. 2. Rome: Food and Agriculture Organization of the United Nations. p 1046–155. Schubart C, Reuschel S. (2009). A proposal for a new classification of Portunoidea and Cancroidea (Brachyura: Heterotremata) based on two independent molecular phylogenies. Decapod Crustacean Phylogenetics. Boca Raton: CRC Press. Spiridonov VA, Neretina TV, Schepetov D. (2014). Morphological characterization and molecular phylogeny of Portunoidea Rafinesque, 1815 (Crustacea Brachyura): Implications for understanding evolution of swimming capacity and revision of the family-level classification. Zool Anz 253:404–29.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae) 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 swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945553
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 10
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: [Deakin University Library]
Date: 05 November 2015, At: 14:04
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945553
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the swimming crab Thalamita crenata (Ru¨ppell, 1830) (Crustacea; Decapoda; Portunidae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and 2School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
Downloaded by [Deakin University Library] at 14:04 05 November 2015
1
Abstract
Keywords
The complete mitochondrial genome of the swimming crab Thalamita crenata was obtained from a partial genome scan using the MiSeq sequencing system. The Thalamita crenata mitogenome has 15,787 base pairs (70% A+T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 897 bp non-coding AT-rich region. This Thalamita mitogenome sequence is the first for the genus and the eighth for the family Portunidae.
Molecular resource, mitogenome, Portunidae
The family Portunidae is a conspicuous and diverse group of crabs that contains a number of well-known shoreline and commercial species including the European shore crab, Carcinus maenas, mud crabs (Scylla) and swimming crabs (Portunus). More than 300 species placed in over 20 genera are recognized from the family (De Grave et al., 2009; Ng et al., 2008). Members of the family have a distinctive flattened dactyl on the fifth leg used for swimming. The taxonomy of the crabs included in the superfamily Portunoidea is contentious at both the family and subfamily levels (Schubart & Reuschel, 2009). We add another mitogenome to those available for the superfamily (8) by providing the first mitogenome for the genus Thalamita. This is the most diverse genus in the family after Portunus (Davie, 2014) and T. crenata, known as the mangrove swimming or spiny rock crab, is a familiar and wide spread species. It inhabits shallow and coastal waters throughout the Indo-Pacific exploiting both soft and hard substrates, where it can be subjected to local fishing pressure (Ng, 1998). We hope these mitochondrial sequences will stimulate evolutionary and population genetic research on these interesting but poorly studied crustaceans and anticipate they will be valuable for addressing taxonomic issues within the superfamily and the genus. An individual of T. crenata was collected from under rocks on the Nightcliff foreshore, Darwin, Northern Territory. The purification of genomic DNA from claw muscle tissue, partial whole genome sequencing (2 150 bp paired-end run), mitogenome assembly and annotation were performed as previously described (Gan et al., 2014). The partial cox1 gene sequence of T. crenata (GenBank accession number: JX398104) was used as the initial bait for MITObim assembly. The complete mitogenome of T. crenata was 15,787 bp in length (GenBank accession number: LK391945) and contains 37 mitochondrial genes and a non-coding AT-rich region of 897 bp in length (Table 1). The mitogenome gene order is typical for brachyuran crabs and is identical to Portunus trituberculatus. The
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 26 June 2014 Accepted 27 June 2014 Published online 4 August 2014
T. crenata mitogenome base composition was 34% A, 35% T, 12% G and 19% C and is most similar in terms of the entire mitogenome to Charbydis japonicus (83.0%) consistent with the current subfamily classification. This is the eighth mitogenome for the Table 1. Annotation of the complete mitochondrial genome of T. crenata. Gene trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta) cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) 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
Strand
Position
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 –
1–66 64–132 136–205 206–1213 1212–1279 1279–1342 1343–1408 1409–2947 2943–3009 3025–3729 3710–3777 3778–3844 3845–4006 4003–4677 4677–5468 5468–5531 5529–5885 5889–5952 5956–6020 6021–6086 6089–6155 6156–6224 6244–6308 6312–6377 6377–8104 8125–9459 9453–9755 9758–9823 9824–9889 9892–10,398 10,398–11,532 11,533–11,598 11,628–12,584 12,590–12,658 12,615–13,973 13,981–14,054 14,057–14,890 14,891–15,787
Length Intergenic Start Stop (bp) nucleotides codon codon Anticodon 66 69 70 1008 68 64 66 1539 67 705 68 67 162 675 792 64 357 64 65 66 67 69 65 66 1728 1335 303 66 66 507 1135 66 957 69 1359 74 834 897
0 3 3 0 2 1 0 0 5 15 20 0 0 4 1 1 3 3 3 0 2 0 19 3 1 20 7 2 0 2 1 0 29 5 44 7 2 0
GAU UUG CAU ATG
TAG UCA GCA GUA
ATG
TAA
ATG
TAA
UAA UUU GUC ATG ATA ATG
TAG TAA TAA
ATA
TAA
UCC UGC UCG GUU UCU UUC GUG GAA ATG ATG ATG
TAA TAG TAA UGU UGG
ATG ATG
TAA T
ATT
TAG
UGA UAG UAC
2
M. H. Tan et al.
family Portunidae, although four of these are from one genus (Scylla). Our sample is identical to a specimen of T. crenata sequenced for a 527 bp fragment of the cox1 gene (JX398104; Spiridonov et al., 2014). Comparison with the cox1 sequences on the BOLD, however suggests there are major taxonomic issues that need to be addressed at the species and generic levels as samples labeled as T. crenata show very high levels of intra-specific divergences (data can be provided upon request).
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.
Downloaded by [Deakin University Library] at 14:04 05 November 2015
References Davie P. (2014). Thalamita Latreille, 1892 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼106931 (Accessed 06 December 2014).
Mitochondrial DNA, Early Online: 1–2
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. 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. Ng PKL. (1998). Crabs. In: Carpenter KE, Niem VH, editors. The living marine resources of the Western Central Pacific. Vol. 2. Rome: Food and Agriculture Organization of the United Nations. p 1046–155. Schubart C, Reuschel S. (2009). A proposal for a new classification of Portunoidea and Cancroidea (Brachyura: Heterotremata) based on two independent molecular phylogenies. Decapod Crustacean Phylogenetics. Boca Raton: CRC Press. Spiridonov VA, Neretina TV, Schepetov D. (2014). Morphological characterization and molecular phylogeny of Portunoidea Rafinesque, 1815 (Crustacea Brachyura): Implications for understanding evolution of swimming capacity and revision of the family-level classification. Zool Anz 253:404–29.
