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 stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae) 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 stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947587
Published online: 08 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: [Universite Laval]
Date: 06 November 2015, At: 03:53
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947587
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor, Malaysia
Downloaded by [Universite Laval] at 03:53 06 November 2015
1
Abstract
Keywords
The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
Crabs, Menippidae, mitogenome
Stone crabs placed in the family Menippidae can be an important component of the benthic invertebrate fauna in many parts of the world. These include commercially-important species such as the American stone crab (Menippe mercenaria) and one of the largest crabs in the world, Pseudocarcinus gigas (Davie, 2002; Ng et al., 2008). The higher level systematics of this group has been contentious with a number of contrasting views on appropriate arrangements at the subfamily, family and superfamily levels (Karasawa & Schweitzer, 2006; Lai et al., 2014; Ng et al., 2008). Surprisingly mitogenome resources for this family, its relatives and the Brachyura more generally are limited with only 20 crab mitogenomes recorded on GenBank (Shen et al., 2013). The family Menippidae, as it is currently conceived, comprises five genera and 14 species (Davie, 2014). One of these genera is
History Received 9 July 2014 Accepted 19 July 2014 Published online 8 August 2014
Myomenippe, comprising two species distributed in tropical waters of the Indo-Pacific. Myomenippe fornasinii is a littlestudied species, which has a wide distribution across northern Australia. To provide additional molecular resources for the study of the taxonomy and evolutionary history of crabs of the family Menippidae and the Brachyura more generally, we have sequenced the complete mitochondrial genome of M. fornasinii. The M. fornasinii sample was caught from under rocks on the Nightcliff intertidal zone, Darwin, Northern Territory. The purification of genomic DNA from ethanol-preserved leg muscle tissue, 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
Table 1. Annotation of the complete mitochondrial genome of M. fornasinii. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct)
Strand H H H H H H H H H H H H H H
Position 1–1539 1535–1599 1606–2310 2291–2358 2359–2421 2422–2580 2574–3248 3248–4037 4038–4103 4101–4457 4460–4525 4528–4590 4591–4655 4659–4724
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
1539 65 705 68 63 159 675 790 66 357 66 63 65 66
0 5 6 20 0 0 7 1 0 3 2 2 0 3
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
ATG ATT ATG
TAG TAA T
ATA
TAA
UCC UGC UCG GUU UCU (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 [Universite Laval] at 03:53 06 November 2015
Gene 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 L L L L L H L H H H L L L L L – H L H H H L L
4726–4793 4812–4874 4875–4940 4971–6666 6714–8048 8042–8344 8347–8412 8413–8476 8479–8977 8978–10,112 10,113–10,178 10,192–11,172 11,167–11,235 11,190–12,570 12,553–12,621 12,684–13,508 13,509–14,246 14,247–14,313 14,311–14,379 14,384–14,451 14,452–15,462 15,462–15,530 15,530–15,594 15,595–15,658
68 63 66 1696 1335 303 66 64 499 1135 66 981 69 1381 69 825 738 67 69 68 1011 69 65 64
1 18 0 30 47 7 2 0 2 0 0 13 6 46 18 62 0 0 3 4 0 1 1 0
sequence of Menippe mercenaria (GenBank accession number: HM637974) was used as the initial bait for MITObim assembly. The M. fornasinii mitochondrial genome was 15,658 bp in length (GenBank accession number: LK391943) and has 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 738 bp (Table 1). The base composition was 35% A, 36% T, 10% G and 19% C and the order of genes was identical to the standard gene arrangement for brachyuran crabs. Our sample of M. fornasinii showed a 91% similarity for a fragment of a 588 bp of the COI gene for its sister species Myomenippe hardwickii (GenBank accession number: HM638052; Lai et al., 2014). We anticipate that this mitogenome will be used for further phylogenetic investigations of the family, superfamily (Lai et al., 2014) and the brachyura and decapoda more widely (Shen et al., 2013).
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 metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6.
Start codon
Stop codon
Anticodon UUC GUG GAA
ATG ATG ATG
A TAA TAA UGU UGG
ATT ATG
T T
ATA
TAA
UGA UAG UAC GAU UUG CAU ATG
TAA UCA GCA GUA
Davie P. (2014). Menippidae Ortmann, 1893 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼196163 (Accessed 4 July 2014). Davie PJF. (2002). Crustacea: Malacostraca. Eucarida (Part 2). Decapoda – Anomura, Brachyura: Zoological Catalogue of Australia: CSIRO Publications. Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892105. 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. Karasawa H, Schweitzer CE. (2006). A new classification of the Xanthoidea sensu lato (Crustacea: Decapoda: Brachyura) based on phylogenetic analysis and traditional systematics and evaluation of all fossil Xanthoidea sensu lato. Contr Zool 75: 23–73. Lai JCY, Thoma BP, Clark PF, Felder DL, Ng PKL. (2014). Phylogeny of eriphioid crabs (Brachyura, Eriphioidea) inferred from molecular and morphological studies. Zool Scr 43:52–64. 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. Shen H, Braband A, Scholtz G. (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 66:776–89.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae) 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 stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947587
Published online: 08 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: [Universite Laval]
Date: 06 November 2015, At: 03:53
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947587
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia and 2Monash University Malaysia Genomics Facility, School of Science, Bandar Sunway, Selangor, Malaysia
Downloaded by [Universite Laval] at 03:53 06 November 2015
1
Abstract
Keywords
The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
Crabs, Menippidae, mitogenome
Stone crabs placed in the family Menippidae can be an important component of the benthic invertebrate fauna in many parts of the world. These include commercially-important species such as the American stone crab (Menippe mercenaria) and one of the largest crabs in the world, Pseudocarcinus gigas (Davie, 2002; Ng et al., 2008). The higher level systematics of this group has been contentious with a number of contrasting views on appropriate arrangements at the subfamily, family and superfamily levels (Karasawa & Schweitzer, 2006; Lai et al., 2014; Ng et al., 2008). Surprisingly mitogenome resources for this family, its relatives and the Brachyura more generally are limited with only 20 crab mitogenomes recorded on GenBank (Shen et al., 2013). The family Menippidae, as it is currently conceived, comprises five genera and 14 species (Davie, 2014). One of these genera is
History Received 9 July 2014 Accepted 19 July 2014 Published online 8 August 2014
Myomenippe, comprising two species distributed in tropical waters of the Indo-Pacific. Myomenippe fornasinii is a littlestudied species, which has a wide distribution across northern Australia. To provide additional molecular resources for the study of the taxonomy and evolutionary history of crabs of the family Menippidae and the Brachyura more generally, we have sequenced the complete mitochondrial genome of M. fornasinii. The M. fornasinii sample was caught from under rocks on the Nightcliff intertidal zone, Darwin, Northern Territory. The purification of genomic DNA from ethanol-preserved leg muscle tissue, 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
Table 1. Annotation of the complete mitochondrial genome of M. fornasinii. Gene cox1 trnL2(taa) cox2 trnK(ttt) trnD(gtc) atp8 atp6 cox3 trnG(tcc) nad3 trnA(tgc) trnR(tcg) trnN(gtt) trnS1(tct)
Strand H H H H H H H H H H H H H H
Position 1–1539 1535–1599 1606–2310 2291–2358 2359–2421 2422–2580 2574–3248 3248–4037 4038–4103 4101–4457 4460–4525 4528–4590 4591–4655 4659–4724
Length (bp)
Intergenic nucleotides
Start codon
Stop codon
1539 65 705 68 63 159 675 790 66 357 66 63 65 66
0 5 6 20 0 0 7 1 0 3 2 2 0 3
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
ATG ATT ATG
TAG TAA T
ATA
TAA
UCC UGC UCG GUU UCU (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 [Universite Laval] at 03:53 06 November 2015
Gene 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 L L L L L H L H H H L L L L L – H L H H H L L
4726–4793 4812–4874 4875–4940 4971–6666 6714–8048 8042–8344 8347–8412 8413–8476 8479–8977 8978–10,112 10,113–10,178 10,192–11,172 11,167–11,235 11,190–12,570 12,553–12,621 12,684–13,508 13,509–14,246 14,247–14,313 14,311–14,379 14,384–14,451 14,452–15,462 15,462–15,530 15,530–15,594 15,595–15,658
68 63 66 1696 1335 303 66 64 499 1135 66 981 69 1381 69 825 738 67 69 68 1011 69 65 64
1 18 0 30 47 7 2 0 2 0 0 13 6 46 18 62 0 0 3 4 0 1 1 0
sequence of Menippe mercenaria (GenBank accession number: HM637974) was used as the initial bait for MITObim assembly. The M. fornasinii mitochondrial genome was 15,658 bp in length (GenBank accession number: LK391943) and has 37 mitochondrial genes (13 protein-coding genes, 2 rRNAs and 22 tRNAs) and a non-coding region of 738 bp (Table 1). The base composition was 35% A, 36% T, 10% G and 19% C and the order of genes was identical to the standard gene arrangement for brachyuran crabs. Our sample of M. fornasinii showed a 91% similarity for a fragment of a 588 bp of the COI gene for its sister species Myomenippe hardwickii (GenBank accession number: HM638052; Lai et al., 2014). We anticipate that this mitogenome will be used for further phylogenetic investigations of the family, superfamily (Lai et al., 2014) and the brachyura and decapoda more widely (Shen et al., 2013).
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 metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6.
Start codon
Stop codon
Anticodon UUC GUG GAA
ATG ATG ATG
A TAA TAA UGU UGG
ATT ATG
T T
ATA
TAA
UGA UAG UAC GAU UUG CAU ATG
TAA UCA GCA GUA
Davie P. (2014). Menippidae Ortmann, 1893 [Online]. Available at: http:// www.marinespecies.org/aphia.php?p¼taxdetails&id¼196163 (Accessed 4 July 2014). Davie PJF. (2002). Crustacea: Malacostraca. Eucarida (Part 2). Decapoda – Anomura, Brachyura: Zoological Catalogue of Australia: CSIRO Publications. Gan HM, Tan MH, Eprilurahman R, Austin CM. (2014). The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea. Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2014.892105. 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. Karasawa H, Schweitzer CE. (2006). A new classification of the Xanthoidea sensu lato (Crustacea: Decapoda: Brachyura) based on phylogenetic analysis and traditional systematics and evaluation of all fossil Xanthoidea sensu lato. Contr Zool 75: 23–73. Lai JCY, Thoma BP, Clark PF, Felder DL, Ng PKL. (2014). Phylogeny of eriphioid crabs (Brachyura, Eriphioidea) inferred from molecular and morphological studies. Zool Scr 43:52–64. 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. Shen H, Braband A, Scholtz G. (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 66:776–89.
