Skip to main content

Advertisement

SpringerLink
Log in

Genomic and microarray approaches to coral reef conservation biology

  • Review
  • Published:
Coral Reefs Aims and scope Submit manuscript

Abstract

New technologies based on DNA microarrays and comparative genomics hold great promise for providing the background biological information necessary for effective coral reef conservation and management. Microarray analysis has been used in a wide range of applications across the biological sciences, most frequently to examine simultaneous changes in the expression of large numbers of genes in response to experimental manipulation or environmental variation. Other applications of microarray methods include the assessment of divergence in gene sequences between species and the identification of fast-evolving genes. Arrays are presently available for only a limited range of species, but with appropriate controls they can be used for related species, thus avoiding the considerable costs associated with development of a system de novo. Arrays are in use or preparation to study stress responses, early development, and symbiosis in Acropora and Montastraea. Ongoing projects on several corals are making available large numbers of expressed gene sequences, enabling the identification of candidate genes for studies on gamete specificity, allorecognition and symbiont interactions. Over the next few years, microarray and comparative genomic approaches are likely to assume increasingly important and widespread use to study many aspects of the biology of coral reef organisms. Application of these genomic approaches to enhance our understanding of genetic and physiological correlates during stress, environmental disturbance and disease bears direct relevance to the conservation of coral reef ecosystems.

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

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Adjaye J, Herwig R, Herrmann D, Wruck W, BenKahla A, Brink T, Nowak M, Carnwath J, Hultschig C, Niemann H, Lehrach H (2004) Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics 5:83

    Article  Google Scholar 

  • Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55–65

    Article  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  Google Scholar 

  • Ball EE, Hayward DC, Reece-Hoyes JS, Hislop NR, Samuel G, Saint R, Harrison P L, Miller DJ (2002) Coral development: from classical embryology to molecular control. Int J Dev Biol 46:671–678

    Google Scholar 

  • Bielawski JP, Yang Z (2004) A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol 59:121–132

    Article  Google Scholar 

  • Bowtell D, Sambrook J (2003) DNA microarrays: a molecular cloning manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Brunelle B, Nicholson T, Stephens R (2004) Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis. Genome Biol 5:R42

    Article  Google Scholar 

  • Castillo-Davis CI, Kondrashov FA, Hartl DL, Kulathinal RJ (2004) The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res 14:802–811

    Article  Google Scholar 

  • Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2:65–73

    Article  Google Scholar 

  • Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet Supp 32:490–495

    Article  Google Scholar 

  • Cohen S (2002) Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress. Mol Biol Evol 19:1870–1880

    Google Scholar 

  • Douglas AE (2003) Coral bleaching-how and why? Mar Pollut Bull 46:385–392

    Article  Google Scholar 

  • Edge SE, Morgan MB, Gleason DF, Snell TW (2005) Development of a coral cDNA array to examine gene expression profiles in Montastraea faveolata exposed to environmental stress. Mar Pollut Bull 51:507–523

    Article  Google Scholar 

  • Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868

    Article  Google Scholar 

  • Fairhead C, Dujon B (2006) Structure of Kluyveromyces lactis subtelomeres: duplications and gene content. FEMS Yeast Res 6:428–441

    Article  Google Scholar 

  • Feder ME, Mitchell-Olds T (2003) Evolutionary and ecological functional genomics. Nature Rev Genet 4:651–657

    Article  Google Scholar 

  • Galindo BE, Vacquier VD, Swanson WJ (2003) Positive selection in the egg receptor for abalone sperm lysin. Proc Natl Acad Sci USA 100:4639–4643

    Article  Google Scholar 

  • Gao B, Klein LE, Britten RJ, Davidson EH (1986) Sequence of mRNA coding for bindin, a species-specific sea urchin sperm protein required for fertilization. Proc Natl Acad Sci USA 83:8634–8638

    Article  Google Scholar 

  • Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (2005) (eds) Bioinformatics and computational biology solutions using R and bioconductor. Springer, Heidelberg

  • Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15:674–680

    Article  Google Scholar 

  • Gilad Y, Oshlack A, Rifkin SA (2006) Natural selection on gene expression. Trends Genet 22:456–461

    Article  Google Scholar 

  • Gracey AY, Troll JV, Somero GN (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci USA 98:1993–1998

    Article  Google Scholar 

  • Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR (2004) Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101:16970–16975

    Article  Google Scholar 

  • Harr B (2006) Genomic islands of differentiation between house mouse subspecies. Genome Res 16:730–737

    Article  Google Scholar 

  • Heyward AJ, Negri AP (1999) Natural inducers for coral larval metamorphosis. Coral Reefs 18:273–279

    Article  Google Scholar 

  • Hinchliffe SJ, Isherwood KE, Stabler RA, Prentice MB, Rakin A, Nichols RA, Oyston PCF, Hinds J, Titball RW, Wren BW (2003) Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res 13:2018–2029

    Article  Google Scholar 

  • Iwao K, Fujisawa T, Hatta M (2002) A cnidarian neuropeptide of the GLWamide family induces metamorphosis of reef-building corals in the genus Acropora. Coral Reefs 21:127–129

    Google Scholar 

  • Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283:83–87

    Article  Google Scholar 

  • Ji W, Zhou W, Gregg K, Yu N, Davis S, Davis S (2004) A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res 32:e93

    Article  Google Scholar 

  • Kane M, Jatkoe T, Stumpf C, Lu J, Thomas J, Madore S (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28:4552–4557

    Article  Google Scholar 

  • Kassahn KS, Caley MJ, Ward AC, Connolly AR, Stone G, Crozier RH (in press) Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. Mol Ecol

  • Kim C, Joyce E, Chan K, Falkow S (2002) Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 3: research0065

  • Kimmel AR, Oliver B (2006a) DNA Microarrays Part A: Array Platforms and Wet-Bench Protocols. Methods Enzymol, vol 410

  • Kimmel AR, Oliver B (2006b) DNA Microarrays Part B: Databases and Statistics. Methods Enzymol, vol 411

  • Kortschak RD, Samuel G, Saint R, Miller DJ (2003) EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol 13:2190–2195

    Article  Google Scholar 

  • Krasnov A, Koskinen H, Pehkonen P, Rexroad CE, Afanasyev S, Molsa H (2005) Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics 6:3. doi:10.1186/1471-2164-6-3

    Google Scholar 

  • Kresge N, Vacquier VD, Stout CD (2001) Abalone lysin: the dissolving and evolving sperm protein. Bioessays 23:95–103

    Article  Google Scholar 

  • Le Quere A, Eriksen KA, Rajashekar B, Schutzenbubel A, Canback B, Johansson T, Tunlid A (2006) Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays. Mol Ecol 15:535–550

    Article  Google Scholar 

  • Lecompte O, Ripp R, Puzos-Barbe V, Duprat S, Heilig R, Dietrich J, Thierry JC, Poch O (2001) Genome evolution at the genus level: Comparison of three complete genomes of hyperthermophilic Archaea. Genome Res 11:981–993

    Article  Google Scholar 

  • McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652–654

    Article  Google Scholar 

  • Makalowski W, Zhang JH, Boguski MS (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res 6:846–857

    Article  Google Scholar 

  • Mardis ER (2006) Anticipating the $1,000 genome. Genome Biol 7:112. doi:10.1186/gb-2006-7-7-112

    Google Scholar 

  • Massingham T, Goldman N (2005) Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753–1762

    Article  Google Scholar 

  • Matzkin LM (2005) Activity variation in alcohol dehydrogenase paralogs is associated with adaptation to cactus host use in cactophilic Drosophila. Mol Ecol 14:2223–2231

    Article  Google Scholar 

  • Medhora M, Bousamra M, Zhu DL, Somberg L, Jacobs ER (2002) Upregulation of collagens detected by gene array in a model of flow-induced pulmonary vascular remodeling. Am J Physiol Heart Circ Physiol 282:H414–H422

    Google Scholar 

  • Morse DE, Hooker N, Morse ANC, Jensen RA (1988) Control of larval metamorphosis and recruitment in sympatric agariciid corals. J Exp Mar Biol Ecol 116:193–217

    Article  Google Scholar 

  • Mueller WA, Leitz T (2002) Metamorphosis in the Cnidaria. Can J Zool 80:1755–1771

    Article  Google Scholar 

  • Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM (2001) DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci USA 98:9853–9858

    Article  Google Scholar 

  • Nei M (2005) Selectionism and neutralism in molecular evolution. Mol Biol Evol 22:2318–2342

    Article  Google Scholar 

  • Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet 39:197–218

    Article  Google Scholar 

  • Nunney L, Schuenzel EL (2006) Detecting natural selection at the molecular level: a reexamination of some “classic” examples of adaptive evolution. J Mol Evol 62:176–195

    Article  Google Scholar 

  • Podrabsky JE, Somero GN (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 207:2237–2254

    Article  Google Scholar 

  • Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41–46

    Article  Google Scholar 

  • Popesco MC, Maclaren EJ, Hopkins J, Dumas L, Cox M, Meltesen L, McGavran L, Wyckoff GJ, Sikela JM (2006) Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains. Science 313:1304–1307

    Article  Google Scholar 

  • Powers DA, Schulte PM (1998) Evolutionary adaptations of gene structure and expression in natural populations in relation to a changing environment: a multi-disciplinary approach to address the million-year saga of a small fish. J Exp Zool 282:71–94

    Article  Google Scholar 

  • Renn SC, Aubin-Horth N, Hofmann HA (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5:42. doi:10.1186/1471-2164-5-42

    Google Scholar 

  • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329

    Article  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  Google Scholar 

  • Schwarz J, Brokstein P, Manohar C, Coffroth MA, Szmant A, Medina M (2006) Coral Reef Genomics: Developing tools for the functional genomics of coral symbiosis. Proc 10th Int Coral Reef Symp 274–281

  • Shi P, Zhang J (2006) Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes. Mol Biol Evol 23:292–300

    Article  Google Scholar 

  • Spady TC, Seehausen O, Loew ER, Jordan RC, Kocher TD, Carleton KL (2005) Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Mol Biol Evol 22:1412–1422

    Article  Google Scholar 

  • Stoyanova R, Upson JJ, Patriotis C, Ross EA, Henske EP, Datta K, Boman B, Clapper ML, Knudson AG, Bellacosa A (2004) Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays. J Cell Physiol 201:359–365

    Article  Google Scholar 

  • Suzuki Y, Gojobori T (2003) Analysis of coding sequence. In: Salemi M, Vandamme A-M (eds) The phylogenetic handbook. Cambridge University Press, Cambridge, pp 283–311

    Google Scholar 

  • Suzuki Y, Gojobori T, Nei M (2001) ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17:660–661

    Article  Google Scholar 

  • Swanson WJ, Aquadro CF (2002) Positive darwinian selection promotes heterogeneity among members of the antifreeze protein multigene family. J Mol Evol 54:403–410

    Google Scholar 

  • Swanson WJ, Vacquier VD (2002) The rapid evolution of reproductive proteins. Nat Rev Genet 3:137–14

    Article  Google Scholar 

  • Swanson WJ, Clark AG, Waldrip-Dail HM, Wolfner MF, Aquadro CF (2001) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA 98:7375–7379

    Article  Google Scholar 

  • Tautz D, Schmid KJ (1998) From genes to individuals: developmental genes and the generation of the phenotype. Philos Trans R Soc Lond B 353:231–240

    Article  Google Scholar 

  • Technau U, Rudd S, Maxwell P, Gordon PM, Saina M, Grasso LC, Hayward DC, Sensen CW, Saint R, Holstein TW, Ball EE, Miller DJ (2005) Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends Genet 21:633–639

    Article  Google Scholar 

  • Tennessen JA (2005) Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18:1387–1394

    Article  Google Scholar 

  • Thomas JH, Kelley JL, Robertson HM, Ly K, Swanson WJ (2005) Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc Natl Acad Sci USA 102:4476–4481

    Article  Google Scholar 

  • Tsoi SCM, Cale JM, Bird IM, Ewart V, Brown LL, Douglas S (2003) Use of human cDNA microarrays for identification of differentially expressed genes in Atlantic salmon liver during Aeromonas salmonicida infection. Mar Biotechnol 5:545–554

    Article  Google Scholar 

  • Turner TL, Hahn MW, Nuzhdin SV (2005) Genomic islands of speciation in Anopheles gambiae. PLoS Biology 3:1572–1578

    Article  Google Scholar 

  • Williams TD, Gensberg K, Minchin SD, Chipman JK (2003) A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquatic Toxicol 65:141–157

    Article  Google Scholar 

  • Wu LY, Thompson DK, Li GS, Hurt RA, Tiedje JM, Zhou JZ (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Env Microbiol 67:5780–5790

    Article  Google Scholar 

  • Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503

    Article  Google Scholar 

  • Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917

    Google Scholar 

  • Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3:579–588

    Google Scholar 

  • Yang YH, Speed T (2003) Design of microarray expression experiments. In: Bowtell D, Sambrook J (eds) DNA microarrays: a molecular cloning manual. Cold Spring Harbor Laboratory Press, New York, pp 513–525

    Google Scholar 

  • Yu X-J, Zheng H-K, Wang J, Wang W, Su B (in press) Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. Genomics. doi:10.1016/j.ygeno.2006.05.008

  • Zakon HH, Lu Y, Zwickl DJ, Hillis DM (2006) Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution. Proc Natl Acad Sci USA 103:3675–3680

    Article  Google Scholar 

  • Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479

    Article  Google Scholar 

  • Zhu B, Xu F, Baba Y (2006) An evaluation of linear RNA amplification in cDNA microarray gene expression analysis. Mol Genet Metab 87:71–79

    Article  Google Scholar 

Download references

Acknowledgments

We gratefully acknowledge the contributions of various members of our laboratories and external collaborators, and the support of the Australian Research Council (ARC) both directly to DJM and EEB (Grants A00105431, DP0209460 and DP0344483) and via the Centre for the Molecular Genetics of Development and the Centre of Excellence for Coral Reef Studies.

Author information

Author notes

  1. K. S. Kassahn

    Present address: Institute for Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia

Authors and Affiliations

  1. Mathematical Science Institute, Australian National University, Canberra, ACT, 0200, Australia

    S. Forêt

  2. School of Tropical Biology, James Cook University, Townsville, QLD, 4811, Australia

    K. S. Kassahn

  3. ARC Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, PO Box 475, Canberra, ACT, 2601, Australia

    L. C. Grasso, D. C. Hayward & E. E. Ball

  4. ARC Centre of Excellence in Coral Reef Biology and Comparative Genomics Centre, James Cook University, Townsville, QLD, 4811, Australia

    A. Iguchi & D. J. Miller

Authors
  1. S. Forêt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K. S. Kassahn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. L. C. Grasso
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D. C. Hayward
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Iguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. E. E. Ball
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. D. J. Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to D. J. Miller.

Additional information

Communicated by Biology Editor M. van Oppen.

S. Forêt and K.S. Kassahn contributed equally.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Forêt, S., Kassahn, K.S., Grasso, L.C. et al. Genomic and microarray approaches to coral reef conservation biology. Coral Reefs 26, 475–486 (2007). https://doi.org/10.1007/s00338-007-0206-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00338-007-0206-1

Keywords

Search

Navigation