Skip to main content
SpringerLink
Log in

Phylomitogenomics of Malacostraca (Arthropoda: Crustacea)

  • Published:
Acta Oceanologica Sinica Aims and scope Submit manuscript

Abstract

Along with the sequencing technology development and continual enthusiasm of researchers on the mitochondrial genomes, the number of metazoan mitochondrial genomes reported has a tremendous growth in the past decades. Phylomitogenomics—reconstruction of phylogenetic relationships based on mitochondrial genomic data—is now possible across large animal groups. Crustaceans in the class Malacostraca display a high diversity of body forms and include large number of ecologically and commercially important species. In this study, comprehensive and systematic analyses of the phylogenetic relationships within Malacostraca were conducted based on 86 mitochondrial genomes available from GenBank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement (excluding tRNAs) to pancrustacean ground pattern, including six species from Stomatopoda, three species from Amphipoda, two krill, seven species from Dendrobranchiata (Decapoda), and 36 species from Pleocyemata (Decapoda). However, the other 32 mitochondrial genomes reported exhibit major gene rearrangements. Phylogenies based on Bayesian analyses of nucleotide sequences of the protein-coding genes produced a robust tree with 100% posterior probability at almost all nodes. The results indicate that Amphipoda and Isopoda cluster together (Edriophthalma) (BPP=100). Phylomitogenomic analyses strong support that Euphausiacea is nested within Decapoda, and closely related to Dendrobranchiata, which is also consistent with the evidence from developmental biology. Yet the taxonomic sampling of mitochondrial genome from Malacostraca is very biased to the order Decapoda, with no complete mitochondrial genomes reported from 11 of the 16 orders. Future researches on sequencing the mitochondrial genomes from a wide variety of malacostracans are necessary to further elucidate the phylogeny of this important group of animals. With the increase in mitochondrial genomes available, phylomitogenomics will emerge as an important component in the Tree of Life researches.

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

Similar content being viewed by others

References

  • Anderson S, Bankier A T, Barrell B G, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature, 290(5806): 457–465

    Article  Google Scholar 

  • Bauza-Ribot M M, Jaume D, Juan C, et al. 2009. The complete mitochondrial genome of the subterranean crustacean Metacrangonyx longipes (Amphipoda): a unique gene order and extremely short control region. Mitochondrial DNA, 20(4): 88–99

    Article  Google Scholar 

  • Bauza-Ribot M M, Juan C, Nardi F, et al. 2012. Mitogenomic phylogenetic analysis supports continental-scale vicariance in subterranean thalassoid crustaceans. Curr Biol, 22(21): 2069–2074

    Article  Google Scholar 

  • Bibb M J, Van Etten R A, Wright C T, et al. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell, 26(2): 167–180

    Article  Google Scholar 

  • Boore J L, Lavrov D V, Brown W M. 1998. Gene translocation links insects and crustaceans. Nature, 392(6677): 667–668

    Article  Google Scholar 

  • Calman W T. 1904. On the classification of the Crustacea Malacostraca. Ann Mag Nat Hist, 13(74): 144–158

    Article  Google Scholar 

  • Casanova B. 2003. Ordre des Euphausiacea Dana, 1852. Crustaceana, 76(9): 1083–1121

    Article  Google Scholar 

  • Cook C E. 2005. The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC Genomics, 6: 105

    Article  Google Scholar 

  • Darriba D, Taboada G L, Doallo R, et al. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods, 9(8): 772

    Article  Google Scholar 

  • Gillett C P D T, Crampton-Platt A, Timmermans M J T N, et al. 2014. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (coleoptera: curculionoidea). Mol Biol Evol, 31(8): 2223–2237

    Article  Google Scholar 

  • Gordon I. 1955. Systematic position of the Euphausiacea. Nature, 176(4489): 934–934

    Article  Google Scholar 

  • Gurney R. 1942. Larvae of Decapod Crustacea. London: Ray Society, 115

    Google Scholar 

  • Ito A, Aoki M N, Yokobori S, et al. 2010. The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region. Mitochondrial DNA, 21(5): 183–190

    Article  Google Scholar 

  • Ivey J L, Santos S R. 2007. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene, 394(1–2): 35–44

    Article  Google Scholar 

  • Jex A R, Hall R S, Littlewood D T, et al. 2010. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res, 38(2): 522–533

    Article  Google Scholar 

  • Jondeung A, Karinthanyakit W, Kaewkhumsan J. 2012. The complete mitochondrial genome of the black mud crab, Scylla serrata (Crustacea: Brachyura: Portunidae) and its phylogenetic position among (pan)crustaceans. Mol Biol Rep, 39(12): 10921–10937

    Article  Google Scholar 

  • Ki J S, Dahms H U, Hwang J S, et al. 2009. The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs. Comp Biochem Physiol Part D Genomics Proteomics, 4(4): 290–299

    Article  Google Scholar 

  • Ki J S, Hop H, Kim S J, et al. 2010. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features. Comp Biochem Physiol Part D Genomics Proteomics, 5(2): 105–115

    Article  Google Scholar 

  • Kilpert F, Podsiadlowski L. 2006. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics, 7: 241

    Article  Google Scholar 

  • Kilpert F, Podsiadlowski L. 2010a. The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods. Comp Biochem Physiol Part D Genomics Proteomics, 5(1): 36–44

    Article  Google Scholar 

  • Kilpert F, Podsiadlowski L. 2010b. The mitochondrial genome of the Japanese skeleton shrimp Caprella mutica (Amphipoda: Caprellidea) reveals a unique gene order and shared apomorphic translocations with Gammaridea. Mitochondrial DNA, 21(3–4): 77–86

    Article  Google Scholar 

  • Kim S, Ahn D H, Park J K, et al. 2013a. The complete mitochondrial genome of the Japanese ghost shrimp Nihonotrypaea japonica (Crustacea, Decapoda, Axiidea). Mitochondrial DNA, 24(3): 243–245

    Article  Google Scholar 

  • Kim S, Choi H G, Park J K, et al. 2013b. The complete mitochondrial genome of the subarctic red king crab, Paralithodes camtschaticus (Decapoda, Anomura). Mitochondrial DNA, 24(4): 350–352

    Article  Google Scholar 

  • Kim S, Kim J, Choi H G, et al. 2012a. Complete mitochondrial genome of the northern mauxia shrimp Acetes chinensis (Decapoda, Dendrobranchiata, Sergestoidae). Mitochondrial DNA, 23(1): 28–30

    Article  Google Scholar 

  • Kim S, Lee S H, Park M H, et al. 2011. The complete mitochondrial genome of the American lobster, Homarus americanus (Crustacea, Decapoda). Mitochondrial DNA, 22(3): 4–49

    Google Scholar 

  • Kim S, Park M-H, Jung J-H, et al. 2012b. The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. Zoologica Scripta, 41(3): 281–292

    Article  Google Scholar 

  • Krebes L, Bastrop R. 2012. The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region. Comp Biochem Physiol Part D Genomics Proteomics, 7(2): 201–211

    Article  Google Scholar 

  • Lin F J, Liu Yuan, Sha Zhongli, et al. 2012. Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics, 13: 631

    Article  Google Scholar 

  • Liu Yuan, Cui Zhaoxia. 2010a. 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(5): 2559–2569

    Article  Google Scholar 

  • Liu Yuan, Cui Zhaoxia. 2010b. The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda. Comp Biochem Physiol Part D Genomics Proteomics, 5(3): 190–198

    Article  Google Scholar 

  • Liu Y, Cui Z X. 2011. Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations. Mol Biol Rep, 38(1): 403–410

    Article  Google Scholar 

  • Ma Hongyu, Ma Chuanyan, Li Xincang, et al. 2013. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene, 519(1): 120–127

    Article  Google Scholar 

  • Ma Keyi, Feng Jianbin, Lin Jingyun, et al. 2011. The complete mitochondrial genome of Macrobrachium nipponense. Gene, 487(2): 160–165

    Article  Google Scholar 

  • Maricic T, Whitten M, Paabo S. 2010. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One, 5(11): e14004

    Article  Google Scholar 

  • Martin J W, Davis G E. 2001. An updated classification of the recent Crustacea. Los Angeles, California: Natural History Museum of Los Angeles County, 37

    Google Scholar 

  • Miller A D, Austin C M. 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(3): 565–574

    Article  Google Scholar 

  • Miller A D, Murphy N P, Burridge C P, et al. 2005. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol, 7(4): 339–349

    Article  Google Scholar 

  • Miller A D, Nguyen T T, Burridge C P, et al. 2004. Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene, 331: 65–72

    Article  Google Scholar 

  • Peregrino-Uriarte A B, Varela-Romero A, Muhlia-Almazan A, et al. 2009. The complete mitochondrial genomes of the yellowleg shrimp Farfantepenaeus californiensis and the blue shrimp Litopenaeus stylirostris (Crustacea: Decapoda). Comp Biochem Physiol Part D Genomics Proteomics, 4(1): 45–53

    Article  Google Scholar 

  • Place A R, Feng X, Steven C R, et al. 2005. Genetic markers in blue crabs (Callinectes sapidus): II. Complete mitochondrial genome sequence and characterization of genetic variation. J Exp Mar Biol Ecol, 319(1–2): 15–27

    Article  Google Scholar 

  • Qian Guanshui, Zhao Qiang, Wang An, et al. 2011. Two new decapod (Crustacea, Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda. Zool J Linn Soc, 162(3): 471–481

    Article  Google Scholar 

  • Regier J C, Shultz J W, Kambic R E. 2005. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc Biol Sci, 272(1561): 395–401

    Article  Google Scholar 

  • Richter, Scholtz. 2001. Phylogenetic analysis of the Malacostraca (Crustacea). J Zoolog Syst Evol Res, 39(3): 113–136

    Article  Google Scholar 

  • Ronquist F, Huelsenbeck J P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12): 1572–1574

    Article  Google Scholar 

  • Sars G O. 1883. Preliminary notices on the Schizopoda of H.M.S. “Challenger’s” expedition. Bulletin of the Mauritius Institute, 7: 1–43

    Google Scholar 

  • Segawa R D, 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

    Article  Google Scholar 

  • Shen H, Braband A, Scholtz G. 2013. Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Mol Phylogenet Evol, 66(3): 776–789

    Article  Google Scholar 

  • Shen Xin, Ren Jianfeng, Cui Zhaoxia, et al. 2007. The complete mitochondrial genomes of two common shrimps (Litopenaeus vannamei and Fenneropenaeus chinensis) and their phylogenomic considerations. Gene, 403(1–2): 98–109

    Article  Google Scholar 

  • Shen Xin, Sun Mingan, Wu Zhigang, et al. 2009. The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes. Gene, 437(1–2): 1–8

    Article  Google Scholar 

  • Shen Xin, Wang Haiqing, Ren Jianfeng, et al. 2010. The mitochondrial genome of Euphausia superba (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers. Mol Biol Rep, 37(2): 771–784

    Article  Google Scholar 

  • Shen Xin, Wang Haiqing, Wang Minxiao, et al. 2011. The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats. Genome, 54(11): 911–922

    Article  Google Scholar 

  • Shi Huafeng, Liu Ruiyu, Sha Zhongli, et al. 2012. Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster. Marine Genomics, 6: 7–15

    Article  Google Scholar 

  • Shin S C, Cho J, Lee J K, et al. 2012. Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, Amphipod). Mitochondrial DNA, 23(1): 25–27

    Article  Google Scholar 

  • Sun Hongying, Zhou Kaiya, Song Daxiang. 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

    Article  Google Scholar 

  • Thompson J D, Gibson T J, Plewniak F, et al. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res, 25(24): 4876–4882

    Article  Google Scholar 

  • von Reumont B M, Jenner R A, Wills M A, et al. 2012. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol, 29(3): 1031–1045

    Article  Google Scholar 

  • Wang Jun, Huang Lei, Cheng Qixuan, et al. 2014. Complete mitochondrial genomes of three mitten crabs, Eriocheir sinensis, E. hepuensis, and E. japonica. Mitochondrial DNA, 10: 1–2

    Google Scholar 

  • Wilson K, Cahill V, Ballment E, et al. 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol Biol Evol, 17(6): 863–874

    Article  Google Scholar 

  • Yamauchi M, Miya M, Nishida M. 2002. Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene, 295(1): 89–96

    Article  Google Scholar 

  • Yamauchi M M, Miya M U, Machida R J, et al. 2004. PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar Biotechnol, 6(5): 419–429

    Article  Google Scholar 

  • Yamauchi M M, Miya M U, Nishida M. 2003. Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura). Gene, 311: 129–135

    Article  Google Scholar 

  • Yang C H, Tsang L M, Chu K H, et al. 2012. Complete mitogenome of the deep-sea hydrothermal vent shrimp Alvinocaris chelys Komai and Chan, 2010 (Decapoda: Caridea: Alvinocarididae). Mitochondrial DNA, 23(6): 417–419

    Article  Google Scholar 

  • Yang Jinshu, Lu Bo, Chen Dianfu, et al. 2013. When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans. Mol Biol Evol, 30(2): 305–309

    Article  Google Scholar 

  • Yang J S, Nagasawa H, Fujiwara Y, et al. 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

    Article  Google Scholar 

  • Yang J S, Nagasawa H, Fujiwara Y, et al. 2010. The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): a link between the Bythograeoidea and Xanthoidea. Zoologica Scripta, 39(6): 621–630

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang, 222005, China

    Xin Shen, Mei Tian & Binlun Yan

  2. Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China

    Xin Shen

  3. Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China

    Xin Shen & Kahou Chu

Authors
  1. Xin Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mei Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Binlun Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kahou Chu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xin Shen.

Additional information

Foundation item: The National Natural Science Foundation of China under contract Nos 41476146 and 40906067; Hong Kong Scholars Program under contract No. XJ2012056; China Postdoctoral Science Foundation under contract Nos 2012M510054 and 2012T50218; a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shen, X., Tian, M., Yan, B. et al. Phylomitogenomics of Malacostraca (Arthropoda: Crustacea). Acta Oceanol. Sin. 34, 84–92 (2015). https://doi.org/10.1007/s13131-015-0583-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13131-015-0583-1

Key words

Search

Navigation