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 soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae) 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 soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.982585
Published online: 25 Nov 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 Santa Barbara]
Date: 05 November 2015, At: 19:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982585
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Selangor, Malaysia and 2Genomics Facility, Monash University Malaysia, Selangor, Malaysia
Downloaded by [University of California Santa Barbara] at 19:26 05 November 2015
1
Abstract
Keywords
The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
Crabs, Mictyridae, mitogenome
Soldier crabs belong to the family Mictyridae, one of eight extant families recognized within the superfamily Ocypodoidea. The Ocypodoidea contains about 300 species and includes many familiar species from coastal zones in the tropics such as ghost crabs, fiddler crabs and soldier crabs (De Grave et al., 2009; Ng et al., 2008). Soldier crabs are widely distributed across the central Indo-west Pacific region and are distinctive because they swarm in the hundreds and sometimes thousands on beaches and mud flats during low tides. The family Mictyridae has just a single genus Mictyris with just eight species. However, several new species have been discovered and described in recent years (Davie et al., 2013). Surprisingly, limited genomic and molecular genetic resources are available for this conspicuous group of crabs, which is also true of the superfamily Ocypodoidea more generally. For this superfamily, only a single mitogenome is available for the species Ilyoplax deschampsi (family: Dotillidae) obtained by Ji et al. (2014). Mictyris longicarpus is a less-studied species that is widely distribution across northern Australia. To provide additional molecular resources for the study of the taxonomy and phylogeny of Ocypodoid crabs, we have sequenced the mitogenome of M. longicarpus. The M. longicarpus sample was caught from a sandy beach at the Casuarina beach intertidal zone, Darwin, Northern Territory,
History Received 13 October 2014 Accepted 27 October 2014 Published online 25 November 2014
Australia. The purification of genomic DNA from ethanolpreserved leg muscle tissue and partial whole genome sequencing (2 150 bp paired-end run) were performed as previously described (Gan et al., 2014). De novo assembly of the partial genome was carried out using IDBA-UD (Peng et al., 2012). Contig corresponding to the mitogenome was identified through similarity search against the 16S rRNA partial gene sequence of M. brevidactylus (GenBank Accession Number: AB513630). The mitogenome was then recircularised and annotated following the methods described in Gan et al. (2014). The M. longicarpus mitochondrial genome has 37 mitochondrial genes (13 protein-coding genes, two rRNAs and 22 tRNAs), a non-coding region of 636 bp (Table 1) and is 15,548 bp in length (GenBank accession number: LN611670). The order of genes is identical to the typical order for brachyuran (Miller et al., 2004; Yamauchi et al., 2003) with a base composition of 32% A, 37% T, 12% G and 19% C. The M. longicarpus sample shows a 89% similarity to a fragment of a 658 bp cox1 gene for the Asian species Mictyris thailandensis (GenBank accession number: AB795403) (Davie et al., 2013). The M. longicarpus mitogenome will be a valuable resource for taxonomic and phylogenetic investigations of the family, the superfamily and the decapoda more widely (Bracken-Grissom et al., 2013; Shen et al., 2013).
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. Annotation of the complete mitochondrial genome of M. longicarpus.
Downloaded by [University of California Santa Barbara] at 19:26 05 November 2015
Gene 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 trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta)
Strand
Position
Length (bp)
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 – H L H H H L L
1–1539 1535–1599 1606–2313 2294–2362 2364–2430 2431–2589 2583–3257 3257–4055 4056–4119 4117–4470 4469–4532 4535–4599 4598–4664 4670–4736 4736–4805 4806–4872 4873–4938 4939–6667 6714–8051 8045–8347 8350–8416 8417–8483 8462–9013 8994–10,128 10,129–10,197 10,223–11,161 11,192–11,258 11,202–12,583 12,590–12,660 12,661–13,486 13,487–14,122 14,123–14,189 14,187–14,255 14,254–14,322 14,323–15,333 15,333–15,401 15,411–15,474 15,475–15,540
1539 65 708 69 67 159 675 799 64 354 64 65 67 67 70 67 66 1729 1338 303 67 67 552 1135 69 939 67 1382 71 826 636 67 69 69 1011 69 64 66
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 Bracken-Grissom H, Cannon M, Cabezas P, Feldmann R, Schweitzer C, Ahyong S, Felder D, et al. (2013). A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evol Biol 13:128. Davie PJ, Wisespongpand P, Shih H-T. (2013). A new species of Mictyris Latreille, 1806 (Crustacea: Decapoda: Brachyura: Mictyridae) from the Andaman coast of Thailand, with notes on its ecology and behaviour. Zootaxa 3686:65–76. 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. Raffles Bull Zool 21:1–109. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and
Intergenic nucleotides 8 5 6 20 1 0 7 1 0 3 2 2 2 5 1 0 0 0 46 7 2 0 22 20 0 25 30 57 6 0 0 0 3 2 0 1 9 0
Start codon
Stop codon
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
GTG ATT ATG
TAA TAA T
ATA
TAA
UCC UGC UCG GUU UCU UUC GUG GAA ATG ATG ATG
T TAA TAA UGU UGG
ATT ATG
TAA T
ATA
TAA
UGA UAG UAC GAU UUG CAU ATG
TAA UCA GCA GUA
confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Ji Y-K, Wang A, Lu X-L, Song D-H, Jin Y-H, Lu J-J, Sun H-Y. (2014). Mitochondrial genomes of two brachyuran crabs (Crustacea: Decapoda) and phylogenetic analysis. J Crustacean Biol 34:494–503. Miller AD, Nguyen TTT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): A novel gene order revealed. Gene 331:65–72. Ng PKL, Guinot D, Davie P. (2008). Systema Brachyurorum: Part 1. An annotated checklist of extant brachyuran crabs of the world. Raffles Bull Zool 17:1–286. 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 H, Braband A, Scholtz G. (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 66:776–89. Yamauchi MM, Miya MU, Nishida M. (2003). Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene 311:129–35.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae) 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 soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.982585
Published online: 25 Nov 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 Santa Barbara]
Date: 05 November 2015, At: 19:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982585
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae) Mun Hua Tan1,2, Han Ming Gan1,2, Yin Peng Lee1,2, and Christopher M. Austin1,2 School of Science, Monash University Malaysia, Selangor, Malaysia and 2Genomics Facility, Monash University Malaysia, Selangor, Malaysia
Downloaded by [University of California Santa Barbara] at 19:26 05 November 2015
1
Abstract
Keywords
The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
Crabs, Mictyridae, mitogenome
Soldier crabs belong to the family Mictyridae, one of eight extant families recognized within the superfamily Ocypodoidea. The Ocypodoidea contains about 300 species and includes many familiar species from coastal zones in the tropics such as ghost crabs, fiddler crabs and soldier crabs (De Grave et al., 2009; Ng et al., 2008). Soldier crabs are widely distributed across the central Indo-west Pacific region and are distinctive because they swarm in the hundreds and sometimes thousands on beaches and mud flats during low tides. The family Mictyridae has just a single genus Mictyris with just eight species. However, several new species have been discovered and described in recent years (Davie et al., 2013). Surprisingly, limited genomic and molecular genetic resources are available for this conspicuous group of crabs, which is also true of the superfamily Ocypodoidea more generally. For this superfamily, only a single mitogenome is available for the species Ilyoplax deschampsi (family: Dotillidae) obtained by Ji et al. (2014). Mictyris longicarpus is a less-studied species that is widely distribution across northern Australia. To provide additional molecular resources for the study of the taxonomy and phylogeny of Ocypodoid crabs, we have sequenced the mitogenome of M. longicarpus. The M. longicarpus sample was caught from a sandy beach at the Casuarina beach intertidal zone, Darwin, Northern Territory,
History Received 13 October 2014 Accepted 27 October 2014 Published online 25 November 2014
Australia. The purification of genomic DNA from ethanolpreserved leg muscle tissue and partial whole genome sequencing (2 150 bp paired-end run) were performed as previously described (Gan et al., 2014). De novo assembly of the partial genome was carried out using IDBA-UD (Peng et al., 2012). Contig corresponding to the mitogenome was identified through similarity search against the 16S rRNA partial gene sequence of M. brevidactylus (GenBank Accession Number: AB513630). The mitogenome was then recircularised and annotated following the methods described in Gan et al. (2014). The M. longicarpus mitochondrial genome has 37 mitochondrial genes (13 protein-coding genes, two rRNAs and 22 tRNAs), a non-coding region of 636 bp (Table 1) and is 15,548 bp in length (GenBank accession number: LN611670). The order of genes is identical to the typical order for brachyuran (Miller et al., 2004; Yamauchi et al., 2003) with a base composition of 32% A, 37% T, 12% G and 19% C. The M. longicarpus sample shows a 89% similarity to a fragment of a 658 bp cox1 gene for the Asian species Mictyris thailandensis (GenBank accession number: AB795403) (Davie et al., 2013). The M. longicarpus mitogenome will be a valuable resource for taxonomic and phylogenetic investigations of the family, the superfamily and the decapoda more widely (Bracken-Grissom et al., 2013; Shen et al., 2013).
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. Annotation of the complete mitochondrial genome of M. longicarpus.
Downloaded by [University of California Santa Barbara] at 19:26 05 November 2015
Gene 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 trnI(gat) trnQ(ttg) trnM(cat) nad2 trnW(tca) trnC(gca) trnY(gta)
Strand
Position
Length (bp)
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 – H L H H H L L
1–1539 1535–1599 1606–2313 2294–2362 2364–2430 2431–2589 2583–3257 3257–4055 4056–4119 4117–4470 4469–4532 4535–4599 4598–4664 4670–4736 4736–4805 4806–4872 4873–4938 4939–6667 6714–8051 8045–8347 8350–8416 8417–8483 8462–9013 8994–10,128 10,129–10,197 10,223–11,161 11,192–11,258 11,202–12,583 12,590–12,660 12,661–13,486 13,487–14,122 14,123–14,189 14,187–14,255 14,254–14,322 14,323–15,333 15,333–15,401 15,411–15,474 15,475–15,540
1539 65 708 69 67 159 675 799 64 354 64 65 67 67 70 67 66 1729 1338 303 67 67 552 1135 69 939 67 1382 71 826 636 67 69 69 1011 69 64 66
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 Bracken-Grissom H, Cannon M, Cabezas P, Feldmann R, Schweitzer C, Ahyong S, Felder D, et al. (2013). A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evol Biol 13:128. Davie PJ, Wisespongpand P, Shih H-T. (2013). A new species of Mictyris Latreille, 1806 (Crustacea: Decapoda: Brachyura: Mictyridae) from the Andaman coast of Thailand, with notes on its ecology and behaviour. Zootaxa 3686:65–76. 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. Raffles Bull Zool 21:1–109. Gan HM, Schultz MB, Austin CM. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and
Intergenic nucleotides 8 5 6 20 1 0 7 1 0 3 2 2 2 5 1 0 0 0 46 7 2 0 22 20 0 25 30 57 6 0 0 0 3 2 0 1 9 0
Start codon
Stop codon
ATG
TAA
ATG
TAA
Anticodon UAA UUU GUC
GTG ATT ATG
TAA TAA T
ATA
TAA
UCC UGC UCG GUU UCU UUC GUG GAA ATG ATG ATG
T TAA TAA UGU UGG
ATT ATG
TAA T
ATA
TAA
UGA UAG UAC GAU UUG CAU ATG
TAA UCA GCA GUA
confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 14:19. Ji Y-K, Wang A, Lu X-L, Song D-H, Jin Y-H, Lu J-J, Sun H-Y. (2014). Mitochondrial genomes of two brachyuran crabs (Crustacea: Decapoda) and phylogenetic analysis. J Crustacean Biol 34:494–503. Miller AD, Nguyen TTT, Burridge CP, Austin CM. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): A novel gene order revealed. Gene 331:65–72. Ng PKL, Guinot D, Davie P. (2008). Systema Brachyurorum: Part 1. An annotated checklist of extant brachyuran crabs of the world. Raffles Bull Zool 17:1–286. 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 H, Braband A, Scholtz G. (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol 66:776–89. Yamauchi MM, Miya MU, Nishida M. (2003). Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene 311:129–35.
