Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
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The Complete Mitochondrial Genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): Non-Monophylies of Maxillopoda and Crustacea

  • Lim, Jong Tae (Department of Biology, Teachers College, Kyungpook National University) ;
  • Hwang, Ui Wook (Department of Biology, Teachers College, Kyungpook National University)
  • Received : 2006.08.23
  • Accepted : 2006.10.10
  • Published : 2006.12.31
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Abstract

The whole mitochondrial genome (14,915 nt) of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia, Thoracica) was sequenced and characterized. It is the shortest of the 31 completely sequenced crustacean mitochondrial genomes, with the exception of a copepod Tigriopus japonicus (14,628 nt). It consists of the usual 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 relatively short non-coding region (294 nt). The thoracican cirripeds apart from Megabalanus volcano have the same arrangement of protein-coding genes as Limulus polypemus, but there are frequent tRNA gene translocations (at least 8). Some interesting translocation features that may be specific to the thoracican cirriped lineage are as follows: 1) trnK-trnQ lies between the control region and trnI, 2) trnA-trnE lies between trnN and trnS1, 3) trnP lies between ND4L and trnT, and 4) trnY-trnC lies between trnS2 and ND1. In P. mitella there are two trnL genes (L1 and L2) in the typical crustacean positions (ND1-L1-LrRNA and CO1-L2-CO2). The present result is compared and discussed with the other three cirriped mitochondrial genomes from one pedunculate (Pollicipes polymerus) and two sessiles (Tetraclita japonica and M. volcano) published so far. Mitochondrial protein phylogenies reconstructed by the BI and ML algorithms show that the thoracican Cirripedia is monophyletic (BPP 100/BP 100) and associated with Remipedia (BPP 98/BP 35). In addition, Oligostraca, including Ostracoda, Branchiura, and Pentastomida, is a monophyletic group (BPP 99/BP 68), and is basal to all the other examined arthropods. Remipedia + Cirripedia appears as an independent lineage within Arthropoda, apart from Thoracopoda (Malacostraca, Branchiopda, and Cephalocarida). The Thoracopoda is paraphyletic to Hexapoda. The present result suggests that the monophylies of Crustacea and Maxillopoda should be reconsidered.

Keywords

Acknowledgement

Supported by : Korea Research Foundation, Korea Science and Engineering Foundation

References

  1. Abascal, F., Zardoya, R., and Posada, D. (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 12, 12
  2. Boore, J. L. (1999) Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767−1780
  3. Boore, J. L., Lavrov, D. V., and Brown, W. M. (1998) Gene translocation links insects and crustaceans. Nature 392, 667−668
  4. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540−552
  5. Cook, C. E. (2005) The complete mitochondrial genome of the stomatopod crustacean Squilla mantis. BMC genomics 6, 105 https://doi.org/10.1186/1471-2164-6-105
  6. Crozier, R. H. and Crozier, Y. C. (1993) The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133, 97−117
  7. Darwin, C. R. (1851) Fossil Cirripedia. A monograph on the fossil Lepadidae, or, pedunculated cirripedes of Great Britain. in Palaeontographical Society. London
  8. Darwin, C. R. (1854) Fossil Cirripedia. A monograph of the fossil Balanidae and Verrucidae of Great Britain. Palaeontographical Society. London
  9. Giribet, G., Edgecombe, D., and Wheeler, W. C. (2001) Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157−161
  10. Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696−704 https://doi.org/10.1080/10635150390235520
  11. Hassanin, A. (2006) Phylogeny of Arthropoda inferred from mitochondrial sequences: Strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol. Phylogenet. Evol. 38, 100−116 https://doi.org/10.1016/j.ympev.2005.09.012
  12. Hickerson, M. J. and Cummingham, C. W. (2000) Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura). Mol. Biol. Evol. 17, 639−644
  13. Huelsenbeck, J. P. and Ronquist, F. (2001) MrBays: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754−755
  14. Hwang, U. W., Friedrich, M., Tautz, D., Park, C. J., and Kim, W. (2001) Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413, 154−157
  15. Lavrov, D. V., Brown, W. M., and Boore, J. L. (2004) Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc. R. Lond. B. 271, 537−544
  16. Lowe, T. M. and Eddy, S. R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955−964 https://doi.org/10.1093/nar/25.5.955
  17. Machida, R. J., Miya, M. U., and Nishida, S. (2002) Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar. Biotechnol. 4, 406−417
  18. Mallatt, J. M., Garey, J. R., and Shultz, J. W. (2004) Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31, 178−191 https://doi.org/10.1016/j.ympev.2003.07.013
  19. Mau, B., Newton, M. A., and Larget, B. (1999) Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics 55, 1−12 https://doi.org/10.1111/j.0006-341X.1999.00001.x
  20. Nardi, F., Spinsanti, G., Boore, J. L., Carapelli, A., Dallai, R., et al. (2003) Hexapod origins: monophyletic or paraphyletic? Science 299, 1887−1889 https://doi.org/10.1126/science.1078607
  21. Ojala, D., Merkel, C., Gelfand, R., and Attardi, G. (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22, 393−403
  22. Park, J.-K., Choe, B. L., and Eom, K. S. (2004) Two mitochondrial lineages in Korean freshwater corbicula (Corbiculidae: Bivalvia). Mol. Cells 17, 410−414
  23. Peterson, K. J. and Eernisse, D. J. (2001) Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3, 170−205
  24. Schram, F. R. and Hof, C. H. J. (1998) In Arthropod Fossils and Phylogeny, G. D. Edgecombe, G. D. (ed.), pp. 233−302, Columbia Univ. Press, New York
  25. Shao, R., Campbell, N. J. H., and Barker, S. C. (2001) Numerous gene arrangements in mitochondrial genome of the wallaby louse, Heterodoxus marcropus (Phthiraptera). Mol. Biol. Evol. 18, 858−865
  26. Spears, T. and Abele, L. G. (1998) Crustacean phylogeny inferred from 18S rDNA; in Arthropod relationships, Fortey, R. A. and Thomas, R. H. (eds.), pp. 169−187, Chapman & Hall, London
  27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid. Res. 25, 4876−4882 https://doi.org/10.1093/nar/25.24.4876
  28. Wills, M. A. (1998) A phylogeny of Recent and fossil Crustacea derived from morphological characters; in Arthropod relationships, R. A. Fortey and R. H. Thomas (eds.), pp. 189−209, Chapman & Hall, London
  29. Wilson, K., Cahill, V., Ballment, E., and Benzie, J. (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. Miol. Evol. 17, 863−874
  30. Yamauchi, M. M., Miya, M. U., and Nishida, M. (2002) Complete mitochondrial DNA sequence of Japanese spiny lobster, Panulinus japonicus (Crustacea: Decapoda). Gene 295, 89−96
  31. Zrzavy, J., Hypsa, V., and Vlaskova, M. (1998) Arthropod phylogeny: taxonomic congruence, total evidence and conditional combination approaches to morphological and molecular data sets; in Arthropod relationships, Fortey, R. A. and Thomas, R. H. (eds.), pp. 97−10, Chapman & Hall, London