Skip to main content
SpringerLink
Log in

Bioinformatic Techniques on Marine Genomics

  • Chapter
Springer Handbook of Marine Biotechnology

Part of the book series: Springer Handbooks ((SHB))

  • 8710 Accesses

Abstract

Marine biotechnology is the industrial, medical or environmental application of biological resources from the sea. Since the marine environment is the most biologically and chemically diverse habitat on the planet, marine biotechnology has in recent years delivered a growing number of major therapeutic products, industrial and environmental applications, and analytical tools. These range from the use of a snail toxin to develop a pain control drug to metabolites from a sea squirt to develop anticancer therapeutic and marine enzymes to remove bacterial biofilms. In addition, well-known and broadly used analytical techniques are derived from marine molecules or enzymes, including green fluorescence protein gene tagging methods and heat resistant polymerases used in the polymerase chain reaction. Advances in bacterial identification, metabolic profiling, and physical handling of cells are being revolutionized by techniques such as mass spectrometric analysis of bacterial proteins. Advances in instrumentation and a combination of these physical advances with progress in proteomics and bioinformatics are accelerating our ability to harness biology for commercial gain. Single cell Raman spectroscopy and microfluidics are two emerging techniques that we try to touch a bit in this chapter. In this chapter, we provide a brief survey and update of the most powerful and rapidly growing analytical techniques as used in marine biotechnology, together with some promising examples of less well-known earlier stage methods which may make a bigger impact in the future.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 269.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 349.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

2-D:

two-dimensional

BLAST:

basic local alignment search tool

CA4:

combretastatin

CAMERA:

community cyber infrastructure for advanced marine microbial ecology research and analysis

CPU:

central processing unit

DNA:

deoxyribonucleic acid

GFP:

green fluorescent protein

GH:

growth hormone

GOS:

Global Ocean Sampling

IMG/M:

Integrated Microbial Genomes and Metagenomes System

MG-RAST:

meta genomics rapid annotation using subsystems technology

MS:

mass spectroscopy

NCBI:

National Center for Biotechnology Information

PAGE:

polyacrylamide gel electrophoresis

PCR:

polymerase chain reaction

SDS:

sodium dodecyl sulfate

UV:

ultraviolet

cDNA:

complementary DNA

iRFP:

near-infrared fluorescent protein

References

  1. G.R. Carvalho, S. Creer, J.M. Allen, F.O. Costa, C.S. Tsigenopoulos, M. Le Goff-Vitry, A. Magoulas, L. Medlin, K. Metfies: Genomics in the discovery and monitoring of marine biodiversity, Adv. Mar. Genomics 1, 1–32 (2010)

    Google Scholar 

  2. A. Szalay, J. Gray: Computing: Science in an exponential world, Nature 440, 413–414 (2006)

    Article  CAS  Google Scholar 

  3. M.L. Metzker: Sequencing technologies the next generation, Nat. Rev. Genet. 11, 31–46 (2010)

    Article  CAS  Google Scholar 

  4. F. Meyer: Genome Sequencing vs. Moore's Law: Cyber challenges for the next decade, CTWatch Q. 2, 20–22 (2006)

    Google Scholar 

  5. Nature America, Inc.: Metagenomics versus Moore's law, Nat. Methods 6, 623 (2009), Editorial

    Article  Google Scholar 

  6. J. Wilkening, A. Wilke, N. Desai, F. Meyer: Using clouds for metagenomics: A case study, IEEE Int. Conf. Cluster Comput. Workshops, New Orleans 2009) pp. 1–6

    Google Scholar 

  7. L.R. Pomeroy: The ocean's food-web, a changing paradigm, BioScience 24, 499–504 (1974)

    Article  Google Scholar 

  8. J.E. Hobbie, R.J. Daley, S. Jasper: Use of nuclepore filtres for counting bacteria by fluorescent microscopy, Appl. Environ. Microbiol. 33, 1225–1228 (1974)

    Google Scholar 

  9. R. Zimmerman, L.A. Meyer-Reil: A new method for fluorescence staining of bacterial populations on membrane filters, Kiel. Meeresforsch. 30, 24–27 (1974)

    Google Scholar 

  10. C.B. Field, M.J. Behrenfeld, J.T. Randerson, P. Falkowski: Primary production of the biosphere: Integrating terrestrial and oceanic components, Science 281, 237–240 (2009)

    Article  Google Scholar 

  11. W.B. Whitman, D.C. Coleman, W.J. Wiebe: Prokaryotes: The unseen majority, Proc. Natl. Acad. Sci. USA 95, 6578–6583 (1998)

    Article  CAS  Google Scholar 

  12. P.A. del Giorgio, C.M. Duarte: Respiration in the open ocean, Nature 420, 379–384 (2002)

    Article  Google Scholar 

  13. E.F. DeLong: Microbial community genomics in the oceans, Nat. Rev. Microbiol. 3, 459–469 (2005)

    Article  CAS  Google Scholar 

  14. C. Médigue, I. Moszer: Annotation, comparison and databases for hundreds of bacterial genomes, Res. Microbiol. 158, 724–736 (2007)

    Article  Google Scholar 

  15. K. Scheibye-Alsing, S. Hoffmann, A. Frankel, P. Jensen, P.F. Stadler, Y. Mang, N. Tommerup, M.J. Gilchrist, A.B. Nygård, S. Cirera, C.B. Jørgensen, M. Fredholm, J. Gorodkin: Sequence assembly, Comput. Biol. Chem. 33, 121–136 (2009)

    Article  CAS  Google Scholar 

  16. R.D. Finn, J. Tate, J. Mistry, P.C. Coggill, S.J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S.R. Eddy, E.L.L. Sonnhammer, A. Bateman: The Pfam protein families database, Nucleic Acids Res. 36, D281–D288 (2008)

    Article  CAS  Google Scholar 

  17. A.S. Juncker, L.J. Jensen, A. Pierleoni, A. Bernsel, M.L. Tress, P. Bork, G. von Heijne, A. Valencia, C.A. Ouzounis, R. Casadio, S. Brunak: Sequence-based feature prediction and annotation of proteins, Genome Biol. 10, 206 (2009)

    Article  Google Scholar 

  18. R. Rentzsch, C.A. Orengo: Protein function prediction – The power of multiplicity, Trends Biotechnol. 27, 210–219 (2009)

    Article  CAS  Google Scholar 

  19. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N.S. Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer, J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives, J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, D.R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H. Mei Lee, J. Duboi, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proctor, B.A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W.R. McCombie, M. de la Bastide, N. Dedhia, H. Blöcker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J.A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D.G. Brown, C.B. Burge, L. Cerutti, H. Chen, D. Church, M. Clamp, R.R. Copley, T. Doerks, S.R. Eddy, E.E. Eichler, T.S. Furey, J. Galagan, J.G.R. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjako, K. Hokamp, W. Jang, L.S. Johnson, T.A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W.J. Kent, P. Kitts, E.V. Koonin, I. Korf, D. Kulp, D. Lancet, T.M. Lowe, A. McLysaght, T. Mikkelsen, J.V. Moran, N. Mulder, V.J. Pollara, C.P. Ponting, G. Schuler, J. Schultz, G. Slater, A.F.A. Smit, E. Stupka, J. Szustakowki, D. Mieg, J. Thierry, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y.I. Wolf, K.H. Wolfe, S. Yang, R. Yeh, F. Collins, M.S. Guyer, J. Peterson, A. Felsenfeld, K.A. Wetterstrand, R.M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D.R. Cox, M.V. Olson, R. Kaul, C. Raymond, N. Shimizu, K. Kawasaki, S. Minoshima, G.A. Evans, M. Athanasiou, R. Schultz, A. Patrinos, M.J. Morgan: Initial sequencing and analysis of the human genome, Nature 409, 860–921 (2001)

    Article  CAS  Google Scholar 

  20. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L.G. Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R. Ji, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, B. Neelam, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z.Y. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S.C. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M.L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N.N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J.F. Abril, R. Guigó, M.J. Campbell, K.V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y. Chiang, M. Coyne, C. Dahlke, A.D. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Venter, M. Wang, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh, X. Zhu: The sequence of the human genome, Science 291, 1304–1351 (2001)

    Article  CAS  Google Scholar 

  21. F. Sanger, S. Nicklen, A.R. Coulson: DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 74, 5463–5467 (1977)

    Article  CAS  Google Scholar 

  22. R.A. Edwards, B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D.M. Peterson, M.O. Saar, S. Alexander, E.C. Alexander Jr., F. Rohwer: Using pyrosequencing to shed light on deep mine microbial ecology, BMC Genomics 7, 57 (2006)

    Article  Google Scholar 

  23. R. Seshadri, S.A. Kravitz, L. Smarr, P. Gilna, M. Frazier: CAMERA: A community resource for metagenomics, PLoS Biology 5, 75 (2007)

    Article  Google Scholar 

  24. J. Handelsman: Metagenomics: Application of genomics to uncultured microorganisms, Microbiol. Mol. Biol. Rev. 68, 669–685 (2004)

    Article  CAS  Google Scholar 

  25. J. Kennedy, J.R. Marchesi, A.D. Dobson: Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges, Appl. Microbiol. Biotechnol. 75, 11–20 (2007)

    Article  CAS  Google Scholar 

  26. S. Yooseph, G. Sutton, D.B. Rusch, A.L. Halpern, S.J. Williamson, K. Remington, J.A. Eisen, K.B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C.S. Miller, H. Li, S.T. Mashiyama, M.P. Joachimiak, C. van Belle, J.M. Chandonia, D.A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B.J. Raphael, V. Bafna, R. Friedman, S.E. Brenner, A. Godzik, D. Eisenberg, J.E. Dixon, S.S. Taylor, R.L. Strausberg, M. Frazier, J.C. Venter: The Sorcerer II Global Ocean Sampling Expedition: Expanding the universe of protein families, PLoS Biology 5, 16 (2007)

    Article  Google Scholar 

  27. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, E.W. Sayers: GenBank, Nucleic Acids Res. 38, D46–51 (2010)

    Article  CAS  Google Scholar 

  28. R. Leinonen, R. Akhtar, E. Birney, J. Bonfield, L. Bower, M. Corbett, Y. Cheng, F. Demiralp, N. Faruque, N. Goodgame, R. Gibson, G. Hoad, C. Hunter, M. Jang, S. Leonard, Q. Lin, R. Lopez, M. Maguire, H. McWilliam, S. Plaister, R. Radhakrishnan, S. Sobhany, G. Slater, P. Ten Hoopen, F. Valentin, R. Vaughan, V. Zalunin, D. Zerbino, G. Cochrane: Improvements to services at the European nucleotide archive, Nucleic Acids Res. 38, D39–D45 (2010)

    Article  CAS  Google Scholar 

  29. S. Ratnasingham, P.D.N. Hebert: BOLD: The Barcode of Life Data System, Mol. Ecol. Notes 7, 355–364 (2007)

    Article  CAS  Google Scholar 

  30. K. Sorimachi, A.J. Jacks, M.F. Le Gal-Co"effet, G. Williamson, D.B. Archer, M.P. Williamson: Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy, J. Mol. Biol. 259, 970–987 (1996)

    Article  CAS  Google Scholar 

  31. P.J. Simpson, D.N. Bolam, A. Cooper, A. Ciruela, G.P. Hazlewood, H.J. Gilbert, M.P. Williamson: A family llb xylan-binding domain has a similar secondary structure to a homologus family lla cellulose-binding domain but different ligand specificity, Structure 7, 853–864 (1999)

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology, YeungNam University, 214-1 Dae dong, 712-749, Gyeongsan, Korea

    A. Mir Bilal

  2. Department of Biotechnology, YeungNam University, 214-1 Dae dong, 712-749, Gyeongsan, Korea

    Inho Choi

  3. Bio-Physio Sensor Technology, Chemistry Department, Pusan National University, 63 beongil Daehakro, 609-735, Busan, Korea

    Yoon-Bo Shim

  4. Chemistry and Chemical Engineering, Yamagata University, 4-3-16 Jonan,Yonezawa, Yamagata, 992-851, Yonezawa, Japan

    H. Mir Sajjad

Authors
  1. A. Mir Bilal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. H. Mir Sajjad
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Inho Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yoon-Bo Shim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to A. Mir Bilal .

Editor information

Editors and Affiliations

  1. Department of Marine-Bio. Convergence Science Specialized Graduate School Science & Technology Convergence Marine Bioprocess Research Center, Pukyong National University, Yongdang Campus, 365, Sinseon-ro, Nam-gu, 608-739, Busan, Korea

    Se-Kwon Kim Prof.

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bilal, A.M., Sajjad, H.M., Choi, I., Shim, YB. (2015). Bioinformatic Techniques on Marine Genomics. In: Kim, SK. (eds) Springer Handbook of Marine Biotechnology. Springer Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-53971-8_10

Download citation

Publish with us

Policies and ethics

Search

Navigation