Animal cells and systems

The Korean Society for Integrative Biology (한국통합생물학회)
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Phylogenetic Analysis of Mitochondrial DNA Control Region in the Swimming Crab, Portunus trituberculatus

  • Cho, Eun-Min (Department of Biological Sciences, Kongju National University) ;
  • Min, Gi-Sik (Department of Biological Sciences, Inha University) ;
  • Kanwal, Sumaira (Department of Biological Sciences, Kongju National University) ;
  • Hyun, Young-Se (Department of Biological Sciences, Kongju National University) ;
  • Park, Sun-Wha (Department of Biological Sciences, Kongju National University) ;
  • Chung, Ki-Wha (Department of Biological Sciences, Kongju National University)
  • Published : 2009.09.30
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Abstract

The control region of mitochondrial DNA (13516-14619) is located between srRNA and $tRNA^{lle}$ gene in swimming crab, Portunus trituberculatus. The present study was investigated the genetic polymorph isms of the control region in samples of P. trituberculatus collected at coastal waters of the Yellow Sea in Korea. A total of 300 substitution and indel polymorphic sites were identified. In addition to SNPs and indel variation, a hypervariable microsatellite motif was also identified at position from 14358 to 14391, which exhibited 10 alleles including 53 different suballeles. When the hypervariable microsatellite motif was removed from the alignment, 95 haplotypes were identified (93 unique haplotypes). The nucleotide and haplotype diversities were ranged from 0.024 to 0.028 and from 0.952 to 1.000, respectively. The statistically significant evidence for geographical structure was not detected from the analyses of neighbor-joining tree and minimum-spanning network, neither. This result suggest that population of P. trituberculatus are capable of extensive gene flow among populations. We believed that the polymorph isms of the control region will be used for informative markers to study phylogenetic relationships of P. trituberculatus.

Keywords

References

  1. Ballard JWO and Rand DM (2005) The population biology of mitochondrial DNA and its phylogenetic implications. Annu Rev Ecol Evol Syst 36: 621-642 https://doi.org/10.1146/annurev.ecolsys.36.091704.175513
  2. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27: 1767-1780 https://doi.org/10.1093/nar/27.8.1767
  3. Bowman TE and Abele LG (1982) Classification of the recent Crustacea. In: Abele LG (ed), The Biology of Crustacea. Vol. 1: Systematics, the Fossil Record, and Biogeography. Academic Press, New York, pp 1-92
  4. Diniz FM, Maclean N, Ogawa M, Cintra IH, and Bentzen P (2005) The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring. Mar Biotechnol (NY) 7: 462-473 https://doi.org/10.1007/s10126-004-4062-5
  5. Feijao PC, Neiva LS, Azeredo-Espin AML, and Lessinger AC (2006) AMiGA: The Arthropodan Mitochondrial Genomes Accessible database. Bioinformatics 22: 902-903 https://doi.org/10.1093/bioinformatics/btl021
  6. Imai H, Fujii Y, and Karakawa J (1999) Analysis of the population structure of the swimming crab, Portunus trituberculatus in the coastal waters of Okayama Prefecture, by RFLPs in the whole region of mitochondrial DNA. Fish Sci 65: 655-656 https://doi.org/10.2331/suisan.65.655
  7. Kilpert F and Podsiadlowski L (2006) The complete mitochondrial genome ofthe common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 7: 241 https://doi.org/10.1186/1471-2164-7-241
  8. Klinbunga S, Khetpu K, Khamnamtong B, and Menasveta P (2007) Genetic heterogeneity of the blue swimming crab (Portunus pelagicus) in Thailand determined by AFLP analysis. Biochem Genet 45: 725-736 https://doi.org/10.1007/s10528-007-9110-1
  9. Lee HY, Yoo JE, Park MJ, Kim CY, and Shin KJ (2008) Genetic characterization and assessment of authenticity of ancient Korean skeletal remains. Hum BioI 80: 239-250 https://doi.org/10.3378/1534-6617-80.3.239
  10. Liu Y, Liu R, Ye L, Liang J, Xuan F, and Xu Q (2009) Genetic differentiation between populations of swimming crab Portunus trituberculatus along the coastal waters of the East China Sea. Hydrobiologia 618: 125-137 https://doi.org/10.1007/s10750-008-9570-2
  11. Oliveira-Neto JF, Boeger WA, Pie MR, Ostrensky A, and Hungria DB (2007) Genetic structure of populations of the mangrove crab Ucides cordatus (Decapoda: Ocypodidae) at local and regional scales. Hydrobiologia 583: 69-76 https://doi.org/10.1007/s10750-006-0472-x
  12. Pie MR, Oliveira-Neto JF, Boeger WA, Ostrensky A, and Baggio RA (2008) The organization of the mitochondrial control region in 2 Brachyuran Crustaceans: Ucides cordatus (Ocypodidae) and Cardisoma guanhumi (Gecarcinidae). J Hered 99: 432-437 https://doi.org/10.1093/jhered/esn024
  13. Place AR, Feng X, Steven CR, Fourcade HM, and Boore JL (2005) Genetic markers in blue crabs (Callinectes sapidus) II:Complete mitochondrial genome sequence and characterization ofvariation. J Exp Mar Biol Ecol 319: 15-27 https://doi.org/10.1016/j.jembe.2004.03.024
  14. Rozas J, Sanchez-DeIBarrio JC, Messeguer X, and Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioirformatics 19: 2496-2497 https://doi.org/10.1093/bioinformatics/btg359
  15. Segawa RD and 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 https://doi.org/10.1016/j.gene.2005.05.020
  16. Shadel GS and Clayton DA (1997) Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem 66: 409-435 https://doi.org/10.1146/annurev.biochem.66.1.409
  17. Tamura K, Dudley J, Nei M, and Kumar S (2007) MEGA4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599 https://doi.org/10.1093/molbev/msm092
  18. Thompson, JD, Gibson Tl, Plewniak F, Jeanmougin F, and Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882 https://doi.org/10.1093/nar/25.24.4876
  19. van Oven M and Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386-394 https://doi.org/10.1002/humu.20921
  20. Xu Q, Liu R, and Liu Y (2009) Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences. J Experimental Mar BioI Ecol 371: 121-129 https://doi.org/10.1016/j.jembe.2009.01.014
  21. Yamauchi MM, Miya MU, and Nishida M (2003) Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea:Decapoda: Brachyura). Gene 311: 129-135 https://doi.org/10.1016/S0378-1119(03)00582-1