Skip to main content
SpringerLink
Log in

Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA His gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780. doi:10.1093/nar/27.8.1767

    Article  CAS  PubMed  Google Scholar 

  2. Parsons TJ, Coble MD (2001) Increasing the forensic discrimination of mitochondrial DNA testing through the analysis of the entire mitochondrial DNA genome. Croat Med J 42:304–309

    CAS  PubMed  Google Scholar 

  3. Boore JL, Medina M, Rosenberg LA (2004) Complete sequences of two highly rearranged molluscan mitochondrial genomes, those of the scaphopod Graptacme eborea and of the bivalve Mytilus edulis. Mol Biol Evol 21:1492–1503. doi:10.1093/molbev/msh090

    Article  CAS  PubMed  Google Scholar 

  4. Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL (2004) Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genome sequences. Mol Phylogenet Evol 33:22–31. doi:10.1016/j.ympev.2004.05.003

    Article  CAS  PubMed  Google Scholar 

  5. Hua J, Li M, Dong P, Xie Q, Bu W (2009) The mitochondrial genome of Protohermes concolorus Yang et Yang 1988 (Insecta: Megaloptera: Corydalidae). Mol Biol Rep. doi:10.1007/s11033-008-9379-0 (in press)

  6. Kim SR, Kim MI, Hong MY, Kim KY, Kang PD, Hwang JS, Han YS, Jin BR, Kim I (2009) The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae). Mol Biol Rep (in press). doi:10.1007/s11033-008-9393-2

  7. Zhou Z, Huang Y, Shin F, Ye H (2009) The complete mitochondrial genome of Deracantha onos (Orthoptera: Bradyporidae). Mol Biol Rep 36:7–12. doi:10.1007/s11033-007-9145-8

    Article  CAS  PubMed  Google Scholar 

  8. Boore JL, Brown WM (1998) Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 8:668–674. doi:10.1016/S0959-437X(98)80035-X

    Article  CAS  PubMed  Google Scholar 

  9. Boore JL, Lavrov DV, Brown WM (1998) Gene translocation links insects and crustaceans. Nature 392:667–668. doi:10.1038/33577

    Article  CAS  PubMed  Google Scholar 

  10. Boore JL, Macey JR, Medina M (2005) Sequencing and comparing whole mitochondrial genomes of animals. Methods Enzymol 395:311–348. doi:10.1016/S0076-6879(05)95019-2

    Article  CAS  PubMed  Google Scholar 

  11. Place AR, Feng X, Steven CR, Fourcade HM, Boore JL (2005) Genetic markers in blue crabs (Callinectes sapidus). II. Complete mitochondrial genome sequence and characterization of genetic variation. J Exp Mar Biol Ecol 319:15–27. doi:10.1016/j.jembe.2004.03.024

    Article  CAS  Google Scholar 

  12. Yamauchi MM, Miya MU, Nishida M (2003) Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene 311:129–135. doi:10.1016/S0378-1119(03)00582-1

    Article  CAS  PubMed  Google Scholar 

  13. Miller AD, Murphy NP, Burridge CP, Austin CM (2005) Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7:339–349. doi:10.1007/s10126-004-4077-8

    Article  CAS  PubMed  Google Scholar 

  14. Sun H, Zhou K, Song D (2005) Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 349:207–217. doi:10.1016/j.gene.2004.12.036

    Article  CAS  PubMed  Google Scholar 

  15. Segawa RD, Aotsuka T (2005) The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene 355:28–39. doi:10.1016/j.gene.2005.05.020

    Article  CAS  PubMed  Google Scholar 

  16. Ng PKL, Guinot D, Davie PJF (2008) Systema Brachyuorum: part I. An annotated checklist of extant Brachyuran crabs of the world. Raffles Bull Zool 17:1–286

    Google Scholar 

  17. Wee DP, Ng PKL (1995) Swimming crabs of the genera Charybdis De Haan, 1833 and Thalamita Latreille, 1829 (Crustacea: Decapoda: Brachyura: Portunidae) from peninsular Malaysia and Singapore. Raffles Bull Zool (Suppl No) 1:1–128

    Google Scholar 

  18. Smith PJ, Webber WR, McVeagh SM, Inglis GJ, Gust N (2003) DNA, morphological identification of an invasive swimming crab Charybdis japonica (A. Milne-Edwards 1861) in New Zealand waters. N Zeal J Mar Fresh 37:753–762

    Article  Google Scholar 

  19. Gust N, Inglis GJ (2006) Adaptive multi-scale sampling to determine an invasive crab’s habitat usage and range in New Zealand. Biol Invasions 8:339–353. doi:10.1007/s10530-004-8243-y

    Article  Google Scholar 

  20. Chu KH, Tong J, Chan T-Y (1999) Mitochondrial cytochrome oxidase I sequence divergence in some Chinese species of Charybdis (Crustacea: Decapoda: Portunidae). Biochem Syst Ecol 27:461–468. doi:10.1016/S0305-1978(98)00115-X

    Article  CAS  Google Scholar 

  21. Gao T, Zhang X, Watanabe S, Fu SR (2004) A preliminary study of mitochondrial DNA 12S rRNA gene sequence of Charybdis japonica and Thalamita prymna. J Ocean Univ China 34:43–47

    CAS  Google Scholar 

  22. Zhang S, Li XL, Cui ZX, Wang HX, Wang CL, Liu XL (2008) The Applications of mitochondrial DNA in phylogeny reconstruction and species identification of portunid crab. Mark Sci 32:9–18

    CAS  Google Scholar 

  23. Martin JW, Davis GE (2001) An updated classification of the recent crustacea. Natural History Museum of Los Angeles County, Los Angeles

    Google Scholar 

  24. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  25. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299

    CAS  PubMed  Google Scholar 

  26. Lavrov DV, Brown WM, Boore JL (2004) Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc R Soc Lond B Biol Sci 271:537–544. doi:10.1098/rspb.2003.2631

    Article  Google Scholar 

  27. Boore JL, Brown WM (2000) Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol Biol Evol 17:87–106

    CAS  PubMed  Google Scholar 

  28. Cheng S, Chang SY, Gravitt P, Respess R (1994) Long PCR. Nature 369:684–685. doi:10.1038/369684a0

    Article  CAS  PubMed  Google Scholar 

  29. Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194. doi:10.1101/gr.8.3.186

    CAS  PubMed  Google Scholar 

  30. Ewing B, Hillier L, Wendl M, Green P (1998) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185. doi:10.1101/gr.8.3.175

    CAS  PubMed  Google Scholar 

  31. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202. doi:10.1101/gr.8.3.195

    CAS  PubMed  Google Scholar 

  32. Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255. doi:10.1093/bioinformatics/bth352

    Article  CAS  PubMed  Google Scholar 

  33. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. doi:10.1093/nar/25.5.955

    Article  CAS  PubMed  Google Scholar 

  34. Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274. doi:10.1007/s00294-007-0161-y

    Article  CAS  PubMed  Google Scholar 

  35. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599. doi:10.1093/molbev/msm092

    Article  CAS  PubMed  Google Scholar 

  36. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. doi:10.1093/nar/25.24.4876

    Article  CAS  PubMed  Google Scholar 

  37. Xia X, Xie Z, Salemi M, Chen L, Wang Y (2003) An index of substitution saturation and its application. Mol Phylogenet Evol 26:1–7. doi:10.1016/S1055-7903(02)00326-3

    Article  CAS  PubMed  Google Scholar 

  38. Xia X, Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. J Hered 92:371–373. doi:10.1093/jhered/92.4.371

    Article  CAS  PubMed  Google Scholar 

  39. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704. doi:10.1080/10635150390235520

    Article  PubMed  Google Scholar 

  40. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755. doi:10.1093/bioinformatics/17.8.754

    Article  CAS  PubMed  Google Scholar 

  41. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818. doi:10.1093/bioinformatics/14.9.817

    Article  CAS  PubMed  Google Scholar 

  42. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105. doi:10.1093/bioinformatics/bti263

    Article  CAS  PubMed  Google Scholar 

  43. Shen X, Ren J, Cui Z, Sha Z, Wang B, Xiang J, Liu B (2007) The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene 403:98–109. doi:10.1016/j.gene.2007.06.021

    Article  CAS  PubMed  Google Scholar 

  44. Shen X, Sun M, Wu Z, Tian M, Cheng H, Zhao F, Meng X (2009) The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA gene. Gene 437:1–8. doi:10.1016/j.gene.2009.02.014

    Article  CAS  PubMed  Google Scholar 

  45. Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216. doi:10.1016/S0074-7696(08)62066-5

    Article  CAS  PubMed  Google Scholar 

  46. Ojala D, Montoya J, Attardi G (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–474. doi:10.1038/290470a0

    Article  CAS  PubMed  Google Scholar 

  47. Yang JS, Nagasawa H, Fujiwara Y, Tsuchida S, Yang WJ (2008) The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics 9:257. doi:10.1186/1471-2164-9-257

    Article  PubMed  CAS  Google Scholar 

  48. Hickerson MJ, Cunningham CW (2000) Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura). Mol Biol Evol 17:639–644

    CAS  PubMed  Google Scholar 

  49. Miller AD, Nguyen TT, 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. doi:10.1016/j.gene.2004.01.022

    Article  CAS  PubMed  Google Scholar 

  50. Boas JEV (1880) Studier over Decapodernes Slaegtskabsforhold. Kongel Danske Videnske Selsk Skr 6:25–210

    Google Scholar 

  51. Felgenhauer BE, Abele LG (1983) Phylogenetic relationships among shrimp-like decapods. Crustac Issues 1:291–311

    Google Scholar 

  52. Abele LG, Felgenhauer BE (1986) Phylogenetic and phenetic relationships among the lower Decapoda. J Crustac Biol 6:385–400. doi:10.2307/1548179

    Article  Google Scholar 

  53. Abele LG (1991) Comparison of morphological and molecular phylogeny of the Decapoda. Mem Queensl Mus 31:101–108

    Google Scholar 

  54. Burkenroad MD (1963) The evolution of the Eucarida (Crustacea, Eumalacostraca), in relation to the fossil record. Tulane Stud Geol 2:1–17

    Google Scholar 

  55. Burkenroad MD (1981) The higher taxonomy and evolution of Decapoda (Crustacea). Trans San Diego Soc Nat Hist 19:251–268

    Google Scholar 

  56. Tsang LM, Ma KY, Ahyong ST, Chan T-Y, Chu KH (2008) Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia. Mol Phylogenet Evol 48:359–368. doi:10.1016/j.ympev.2008.04.009

    Article  CAS  PubMed  Google Scholar 

  57. Scholtz G, Richter S (1995) Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zool J Linn Soc 113:289–328. doi:10.1111/j.1096-3642.1995.tb00936.x

    Article  Google Scholar 

  58. Schram FR (2001) Phylogeny of decapods: moving towards a consensus. Hydrobiologia 449:1–20. doi:10.1023/A:1017543712119

    Article  Google Scholar 

  59. Dixon CJ, Ahyong ST, Schram FR (2003) A new hypothesis of decapod phylogeny. Crustaceana 76:935–975. doi:10.1163/156854003771997846

    Article  Google Scholar 

  60. Miller AD, Austin CM (2006) The complete mitochondrial genome of the mantid shrimp Harpiosquilla harpax, and a phylogenetic investigation of the Decapoda using mitochondrial sequences. Mol Phylogenet Evol 38:565–574. doi:10.1016/j.ympev.2005.10.001

    Article  CAS  PubMed  Google Scholar 

  61. Ivey JL, Santos SR (2007) The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene 394:35–44. doi:10.1016/j.gene.2007.01.009

    Article  CAS  PubMed  Google Scholar 

  62. Stephenson W, Campbell B (1960) The Australian portunids (Crustacea: Portunidae) IV: remaining genera. Aust J Mar Freshwater Res 11:73–122. doi:10.1071/MF9600073

    Article  Google Scholar 

  63. Dai AY, Yang SL, Song YZ, Chen GX (1986) Crabs of the China seas. China Ocean Press, Beijing

    Google Scholar 

  64. Apel M, Spiridonov VA (1998) Taxonomy and zoogeography of the portunid crabs (Crustacea: Decapoda: Brachyura: Portunidae) of the Arabian Gulf and adjacent waters. Fauna Arabia 17:159–331

    Google Scholar 

  65. Ng PKL, Wang C-H, Ho P-H, Shih H-T (2001) An annotated checklist of brachyuran crabs from Taiwan (Crustacea: Decapoda). Natl Taiwan Mus Spec Publ Ser 11:1–86

    Google Scholar 

Download references

Acknowledgments

We thank Prof. Xinzheng LI for specimen identification and Mr. Ping ZHANG for assistance in bioinformatics analyses. This research was supported by the National Natural Science Foundation of China (no. 40676085) and Chinese National ‘863’ Project (no. 2006AA10A406).

Author information

Authors and Affiliations

  1. EMBL, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China

    Yuan Liu & Zhaoxia Cui

  2. Graduate University of the Chinese Academy of Sciences, 100039, Beijing, China

    Yuan Liu

Authors
  1. Yuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhaoxia Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhaoxia Cui.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, Y., Cui, Z. Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol Biol Rep 37, 2559–2569 (2010). https://doi.org/10.1007/s11033-009-9773-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-009-9773-2

Keywords

Search

Navigation