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Assessing population-level variation in the mitochondrial genome of Euphausia superba using 454 next-generation sequencing

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Abstract

The Antarctic krill (Euphausia superba Dana 1852) is widely distributed throughout the Southern Ocean, where it provides a key link between primary producers and upper trophic levels and supports a major commercial fishery. Despite its ecological and commercial importance, genetic population structure of the Antarctic krill remains poorly described. In an attempt to illuminate genetic markers for future population and phylogenetic analysis, five E. superba mitogenomes, from samples collected west of the Antarctic Peninsula, were sequenced using new 454 next-generation sequencing techniques. The sequences, of lengths between 13,310 and 13,326 base pairs, were then analyzed in the context of two previously-published near-complete sequences. Sequences revealed relatively well-conserved partial mitochondrial genomes which included complete sequences for 11 of 13 protein-coding genes, 16 of 23 tRNAs, and the large ribosomal subunit. Partial sequences were also recovered for cox1 and the small ribosomal subunit. Sequence analysis suggested that the cox2, nad5, and nad6 genes would be the best candidates for future population genetics analyses, due to their high number of variable sites. Future work to reveal the noncoding control region remains.

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References

  1. Laws RM (1985) The ecology of the southern ocean. Am Sci 73:26–40

    Google Scholar 

  2. Watanuki Y, Yoshihisa M, Yasuhiko N (1994) Euphausia superba dominates in the diet of Adélie penguins feeding under fast sea-ice in the shelf areas of Enderby Land in summer. Polar Biol 14(6):429–432. doi:10.1007/BF00240264

    Article  Google Scholar 

  3. Ruiz-Halpern S, Duarte CM, Tovar-Sanchez A, Pastor M, Horstkotte B, Lasternas S, Agustí S (2011) Antarctic krill as a source of dissolved organic carbon to the Antarctic ecosystem. Limnol Oceanogr 56(2):521–528. doi:10.4319/lo.2011.56.2.0521

    Article  CAS  Google Scholar 

  4. Jones CD, Ramm DC (2004) The commercial harvest of krill in the southwest Atlantic before and during the CCAMLR 2000 Survey. Deep Sea Res Part II: Trop Stud Oceanogr 51(12–13):1421–1434. doi:10.1016/j.dsr2.2004.06.009

    Google Scholar 

  5. Siegel V, Loeb V (1995) Recruitment of Antarctic krill Euphausia superba and possible causes for its variability. Mar Ecol Prog Ser 123:45–56. doi:10.3354/meps123045

    Article  Google Scholar 

  6. Loeb V, Siegel V, Holm-Hansen O, Hewitt R, Fraser W, Trivelpiece W, Trivelpiece S (1997) Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387:897–900. doi:10.1038/43174

    Article  CAS  Google Scholar 

  7. Atkinson A, Siegel V, Pakhomov E, Rothery P (2004) Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature 432:100–103. doi:10.1038/nature02996

    Article  PubMed  CAS  Google Scholar 

  8. Zane L, Ostellari L, Maccatrozzo L, Bargelloni L, Battaglia B, Patarnell T (1998) Molecular evidence for genetic subdivision of Antarctic krill (Euphausia superba Dana) populations. Proc R Soc, Lond B 256:2387–2391. doi:10.1098/rspb.1998.0588

    Article  Google Scholar 

  9. Batta-Lona PG, Bucklin A, Wiebe P, Patarnello T, Copley NJ (2010) Population genetic variation of the Southern Ocean krill, Euphausia superba, in the Western Antarctic Peninsula region based on mitochondrial single nucleotide polymorphisms (SNPs). Deep-Sea Res II. 58(13–16):1652–1661. doi:10.1016/j.dsr2.2010.11.017

    Google Scholar 

  10. Goodall-Copestakw WP, Pérez-Espona S, Clark MS, Murphy EJ, Seear PJ, Tarling GA (2010) Swarms of diversity at the gene cox1 in Antarctic krill. Heredity 104:513–518. doi:10.1038/hdy.2009.188

    Article  Google Scholar 

  11. Bortolotto E, Bucklin A, Mezzavilla M, Zane L, Patarnello T (2011) Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba. BMC Genet 12(32). doi:10.1186/1471-2156-12-32

  12. Machida RJ, Masaki UM, Mitsugu MY, Mutsumi N, Nishida S (2004) Organization of the mitochondrial genome of Antarctic Krill Euphausia superba (Crustacea: Malacostraca). Mar Biotechnol 6:238–250. doi:10.1007/s10126-003-0016-6

    Article  PubMed  CAS  Google Scholar 

  13. Shen X, Haiqing W, Ren J, Tian M, Want M (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. doi:10.1007/s11033-009-9602-7

    Article  PubMed  CAS  Google Scholar 

  14. Wilson AC, Cann RL, Carr SM, George EM, Gyllensten UB, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26:40–375. doi:10.1111/j.1095-8312.1985.tb02048.x

    Article  Google Scholar 

  15. Moritz C, Dowling TE, Brown BM (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Ann Rev Ecol Syst 18:269–292. doi:0.1146/annurev.es.18.110187.001413

    Article  Google Scholar 

  16. 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  PubMed  CAS  Google Scholar 

  17. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27(8):1767–1780. doi:10.1093/nar/27.8.1767

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  20. Wyman SK, Jansen RK, Boore JK (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):2353–3255. doi:10.1093/bioinformatics/bth352

    Article  Google Scholar 

  21. Lowe TM, Eddy SR (1997) tRNAscna-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25(5):955–964. doi:10.1093/nar/25.5.955

    Article  PubMed  CAS  Google Scholar 

  22. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95–98

    CAS  Google Scholar 

  23. Frackman S, Kobs G, Simpson D, Storts D (1998) Betaine and DMSO: enhancing agents for PCR. Promega Notes 65:27

  24. Pääbo S, Gifford JA, Wilson AC (1988) Mitochondrial DNA sequences from a 7,000-year old brain. Nucl Acids Res 16(20):9775–9787. doi:10.1093/nar/16.20.9775

    Article  PubMed  Google Scholar 

  25. Sarkar G, Kapelner S, Sommer SS (1990) Formamide can dramatically improve the specificity of PCR. Nucl Acids Res 18(24):7465. doi:10.1093/nar/18.24.7465

    Article  PubMed  CAS  Google Scholar 

  26. Bachmann B, Lüke W, Hunsmann G (1990) Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucl Acids Res 18(5):1309. doi:10.1093/nar/18.5.1309

    Article  PubMed  CAS  Google Scholar 

  27. Chu KH, Li CP, Tam YK, Lavery S (2003) Application of mitochondrial control region in population genetic studies of the shrimp Penaeus. Mol Ecol Note 3(1):120–122. doi:10.1046/j.1471-8286.2003.00376.x

    Article  CAS  Google Scholar 

  28. Diniz FM, Maclean N, Ogawa M, Cintra IHA, Bentzen P (2004) The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring. Mar Biotechnol 7(5):462–473. doi:10.1007/s10126-004-4062-5

    Article  Google Scholar 

  29. Liu Y (2010) Complete mitochondrial genome of the Chinese spiny lobster Panulirus stimpsoni (Crustacea: Decapoda): genome characterization and phylogenetic considerations. Mol Biol Rep 38(1):403–410. doi:10.1007/s11033-010-0122-2

    Article  PubMed  Google Scholar 

  30. Mancini E, De Biase A, Mariottini P, Bellini A, Audisio P (2008) Structure and evolution of the mitochondrial control region of the pollen beetle Meligethes thalassophilous (Coleoptera: Nitidulidae). Genome 51(3):196–207. doi:10.1139/G07-116

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank D. Jacobson, E. Slikas, D. Steel, and A. Alexander for their support with the 454 sequencing and analysis, C. Shaw for the samples used in this study, and M. O’Connor for assistance in constructing our sampling map. This research was co-funded by the ASSURE program of the Department of Defense in partnership with the National Science Foundation REU Site program under Grant No. NSF OCE-1004947.

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Authors and Affiliations

  1. Cooperative Institute for Marine Resources Studies, Hatfield Marine Science Center, Oregon State University, Newport, OR, USA

    Mattias Johansson, Elizabeth Duda, Angela Sremba & Michael Banks

  2. Pomona College, Claremont, CA, USA

    Elizabeth Duda

  3. National Marine Fisheries Service, NOAA, Hatfield Marine Science Center, Newport, OR, USA

    William Peterson

Authors
  1. Mattias Johansson
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  2. Elizabeth Duda
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  3. Angela Sremba
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  4. Michael Banks
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  5. William Peterson
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Correspondence to Mattias Johansson.

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Johansson, M., Duda, E., Sremba, A. et al. Assessing population-level variation in the mitochondrial genome of Euphausia superba using 454 next-generation sequencing. Mol Biol Rep 39, 5755–5760 (2012). https://doi.org/10.1007/s11033-011-1385-y

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  • DOI: https://doi.org/10.1007/s11033-011-1385-y

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