Skip to main content
SpringerLink
Log in

Profiling Transcriptome Complexity and Secondary Metabolite Synthesis in a Benthic Soft Coral, Sinularia polydactyla

  • Original Article
  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

Sinularia polydactyla, an abundant Indo-Pacific soft coral species, exhibits biochemical phenotypic plasticity, prompting investigations into differences in mRNA diversity and complexity in response to predation stress. Changes in transcriptome complexity of S. polydactyla cDNA libraries were measured using reannealing rate assays that employ an informatics-based analysis of kinetic profiles. This method allows for quick, high-throughput analysis of sequence complexity and has been used to compare transcriptome-level differences in other marine invertebrates. Here, S. polydactyla colonies were transplanted between two sites exhibiting high and low predation levels. Statistically significant differences between bite scar counts found on different transplant groups suggest site-specific variation in predation. Changes in mRNA pool complexity were quantified to indicate shifts in secondary metabolite concentration between treatment groups. Examining the complexity of the mRNA pool in this soft coral is one of the first steps toward understanding the mechanisms of phenotypic plasticity at a biochemical and molecular level.

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
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • E Abouheif GA Wray (2002) ArticleTitleEvolution of the gene network underlying wing polymorphism in ants Science 297 249–252 Occurrence Handle10.1126/science.1071468

    Article  Google Scholar 

  • AA Agrawal (2001) ArticleTitlePhenotypic plasticity in the interactions and evolution of species Science 294 321–326 Occurrence Handle10.1126/science.1060701

    Article  Google Scholar 

  • RM Callaway SC Pennings CL Richards (2003) ArticleTitlePhenotypic plasticity and interactions among plants Ecology 84 1115–1128

    Google Scholar 

  • P Chomczynski N Sacchi (1987) ArticleTitleSingle-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction Anal Biochem 162 156–159 Occurrence Handle10.1016/0003-2697(87)90021-2

    Article  Google Scholar 

  • EE Farmer CA Ryan (1992) ArticleTitleOctadecanoid precursors of jasmonic acid activate the synthesis of wound-inducible proteinase inhibitors The Plant Cell 4 129–134 Occurrence Handle10.1105/tpc.4.2.129

    Article  Google Scholar 

  • KT Fielman AG Marsh (2005) ArticleTitleGenome complexity and repetitive DNA in metazoans from extreme marine environments Gene 362 98–108 Occurrence Handle10.1016/j.gene.2005.06.035

    Article  Google Scholar 

  • BG Fleury JC Coll E Tentori S Duquesne L Figueiredo (2000) ArticleTitleEffect of nutrient enrichment on the complementary (secondary) metabolite composition of the soft coral Sarcophyton ehrenbergi (Cnidaria: Octocorallia: Alcyonaceae) of the Great Barrier Reef Mar Biol 136 63–68 Occurrence Handle10.1007/s002270050009

    Article  Google Scholar 

  • AY Gracey AR Cossins (2003) ArticleTitleApplication of microarray technology in environmental and comparative physiology Annu Rev Physiol 65 231–259 Occurrence Handle10.1146/annurev.physiol.65.092101.142716

    Article  Google Scholar 

  • AY Gracey EJ Fraser W Li Y Fang RR Taylor J Rogers A Brass AR Cossins (2004) ArticleTitleCoping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate Proc Natl Acad Sci USA 101 16970–16975 Occurrence Handle10.1073/pnas.0403627101

    Article  Google Scholar 

  • K Hashimoto T Shibuno E Murayama-Kayano H Tanaka T Kayano (2004) ArticleTitleIsolation and characterization of stress-responsive genes from the scleractinian coral Pocillopora damicornis Coral Reefs 23 485–491

    Google Scholar 

  • DA Herms WJ Mattson (1992) ArticleTitleThe dilemma of plants-to grow or defend Q Rev Biol 67 283–335 Occurrence Handle10.1086/417659

    Article  Google Scholar 

  • GE Hofmann JL Burnaford KT Fielman (2005) ArticleTitleGenomics-fueled approaches to current challenges in marine ecology Trends Ecol Evol 20 305–311 Occurrence Handle10.1016/j.tree.2005.03.006

    Article  Google Scholar 

  • HN Kamel FR Fronczek NH Fischer M Slattery (2004) ArticleTitleA novel metabolite from the hybrid soft coral Sinularia maxima × Sinularia polydactyla: a biosynthetically mixed skeleton linking cembrane and africanane terpenoids Tetrahedr Lett 45 1995–1997 Occurrence Handle10.1016/j.tetlet.2003.12.108

    Article  Google Scholar 

  • R Karban IT Baldwin (1997) Induced Responses to Herbivory University of Chicago Press Chicago

    Google Scholar 

  • J Kubanek JR Pawlik TM Eve W Fenical (2000) ArticleTitleTriterpene glycosides defend the Caribbean reef sponge Erylus formosus from predatory fishes Mar Ecol Prog Ser 207 69–77

    Google Scholar 

  • PA Leone BF Bowden AR Carroll JC Coll (1995) ArticleTitleChemical consequences of relocation of the soft coral Lobophytum compactum and its placement in contact with the red alga Plocamium hamatum Mar Biol 122 675–679 Occurrence Handle10.1007/BF00350689

    Article  Google Scholar 

  • JV Lopez CL Peterson R Willoughby AE Wright E Enright S Zoladz JK Reed SA Pomponi (2002) ArticleTitleCharacterization of genetic markers for in vitro cell line indentification of the marine sponge Axinella corrugata J Hered 93 27–36 Occurrence Handle10.1093/jhered/93.1.27

    Article  Google Scholar 

  • AG Marsh KT Fielman (2005) ArticleTitleTranscriptome profiling of individual larvae of two different developmental modes in the poecilogonous polychaete Streblospio benedicti (Spionidae) J Exp Zool 304B 238–249 Occurrence Handle10.1002/jez.b.21037

    Article  Google Scholar 

  • JB McClintock MO Amsler CD Amsler KJ Southworth C Petrie BJ Baker (2004) ArticleTitleBiochemical composition, energy content, and chemical antifeedant and antifoulant defenses of the colonial Antarctic ascidian Distaplia cylindrica Mar Biol 145 885–894 Occurrence Handle10.1007/s00227-004-1388-5

    Article  Google Scholar 

  • HF Nijhout (1999) ArticleTitleControl mechanisms of polyphenic development in insects BioScience 49 181–192 Occurrence Handle10.2307/1313508

    Article  Google Scholar 

  • MF Oleksiak KJ Kolell DL Crawford (2001) ArticleTitleUtility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies Mar Biotechnol 3 S203–S211 Occurrence Handle10.1007/s10126-001-0043-0

    Article  Google Scholar 

  • MF Oleksiak GA Churchill DL Crawford (2002) ArticleTitleVariation in gene expression within and among natural populations Nat Genet 32 261–266 Occurrence Handle10.1038/ng983

    Article  Google Scholar 

  • MF Oleksiak JL Roach DL Crawford (2005) ArticleTitleNatural variation in cardiac metabolism and gene expression in Fundulus heteroclitus Nat Genet 37 67–72

    Google Scholar 

  • H Pavia GB Toth (2000) ArticleTitleInducible chemical resistance to herbivory in the brown seaweed Ascophyllum nodosum Ecology 81 3212–3225 Occurrence Handle10.2307/177411

    Article  Google Scholar 

  • M Pigliucci (2001) Phenotypic Plasticity Beyond Nature and Nurture Johns Hopkins University Press Baltimore

    Google Scholar 

  • JE Podrabsky GN Somero (2004) ArticleTitleChanges 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 Occurrence Handle10.1242/jeb.01016

    Article  Google Scholar 

  • M Puyana W Fenical JR Pawlik (2003) ArticleTitleAre there activated chemical defenses in sponges of the genus Aplysina from the Caribbean Mar Ecol Prog Ser 246 127–135

    Google Scholar 

  • RA Relyea JR Auld (2005) ArticleTitlePredator- and competitor-induced plasticity: how changes in foraging morphology affect phenotypic trade-offs Ecology 86 1723–1729

    Google Scholar 

  • Y Ruan P Ber ParticleLe HH Ng ET Liu (2004) ArticleTitleInterrogating the transcriptome Trends Biotechnol 22 23–30 Occurrence Handle10.1016/j.tibtech.2003.11.002

    Article  Google Scholar 

  • SM Scheiner (1993) ArticleTitleGenetics and evolution of phenotypic plasticity Annu Rev Ecol Syst 24 35–68 Occurrence Handle10.1146/annurev.es.24.110193.000343

    Article  Google Scholar 

  • CE Shannon (1948) ArticleTitleA mathematical theory of communication Bell Syst Tech J 27 379–423

    Google Scholar 

  • M Shpak GA Churchill (2000) ArticleTitleThe information content of a character under a Markov model of evolution Mol Phylogenet Evol 17 231–243 Occurrence Handle10.1006/mpev.2000.0846

    Article  Google Scholar 

  • M Slattery J Starmer VJ Paul (2001) ArticleTitleTemporal and spatial variation in defensive metabolites of the tropical Pacific soft corals Sinularia maxima and S. polydactyla Mar Biol 138 1183–1193 Occurrence Handle10.1007/s002270100540

    Article  Google Scholar 

  • ML Stanton BA Roy DA Thiede (2000) ArticleTitleEvolution in stressful environments. I. Phenotypic variability, phenotypic selection, and response to selection in five distinct environmental stresses Evolution 54 93–111 Occurrence Handle10.1554/0014-3820(2000)054[0093:EISEIP]2.0.CO;2

    Article  Google Scholar 

  • DL Stirewalt EL Pogosova-Agadjanyan N Khalid DR Hare PA Ladne O Sala-Torra LP Zhao JP Radich (2004) ArticleTitleSingle-stranded linear amplification protocol results in reproducible and reliable microarray data from nanogram amounts of starting RNA Genomics 83 321–331 Occurrence Handle10.1016/j.ygeno.2003.08.008

    Article  Google Scholar 

  • MJ Stout KV Workman RM Bostock SS Duffey (1998) ArticleTitleSpecificity of induced resistance in the tomato, Lycopersicon esculentum Oecologia 113 74–81 Occurrence Handle10.1007/s004420050355

    Article  Google Scholar 

  • Y Suzuki HF Nijhout (2006) ArticleTitleEvolution of a polyphenism by genetic accomodation Science 311 650–652 Occurrence Handle10.1126/science.1118888

    Article  Google Scholar 

  • RB Taylor E Sotka ME Hay (2002) ArticleTitleTissue-specific induction of herbivore resistance: seaweed response to amphipod grazing Oecologia 132 68–76 Occurrence Handle10.1007/s00442-002-0944-2

    Article  Google Scholar 

  • JS Thaler AL Fidantsef SS Duffey RM Bostock (1999) ArticleTitleTrade-offs in plant defense against pathogens and herbivores: a field demonstration of chemical elicitors of induced resistance J Chem Ecol 25 1597–1609 Occurrence Handle10.1023/A:1020840900595

    Article  Google Scholar 

  • MA Thomas R Klaper (2004) ArticleTitleGenomics for the ecological toolbox Trends Ecol Evol 19 439–445 Occurrence Handle10.1016/j.tree.2004.06.010

    Article  Google Scholar 

  • GB Toth O Langhamer H Pavia (2005) ArticleTitleInducible and constitutive defenses of valuable seaweed tissues: consequences for herbivore fitness Ecology 86 612–618

    Google Scholar 

  • GC Trussell (1996) ArticleTitlePhenotypic plasticity in an intertidal snail: the role of a common crab predator Evolution 50 448–454 Occurrence Handle10.2307/2410815

    Article  Google Scholar 

  • KL Alstyne ParticleVan GV Wolfe TL Freidenburg A Neill C Hicken (2001) ArticleTitleActivated defense systems in marine macroalgae: evidence for an ecological role for DMSP cleavage Mar Ecol Prog Ser 213 53–65

    Google Scholar 

  • W Weaver (1948) ArticleTitleScience and complexity Am Scientist 36 536

    Google Scholar 

  • A Whitehead DL Crawford (2006a) ArticleTitleNeutral and adaptive variation in gene expression Proc Natl Acad Sci USA 103 5425–5430 Occurrence Handle10.1073/pnas.0507648103

    Article  Google Scholar 

  • A Whitehead DL Crawford (2006b) ArticleTitleVariation within and among species in gene expression: raw material for evolution Mol Ecol 15 1197–1211 Occurrence Handle10.1111/j.1365-294X.2006.02868.x

    Article  Google Scholar 

  • AR Zangerl CE Rutledge (1996) ArticleTitleThe probability of attack and patterns of constitutive and induced defense: a test of optimal defense theory Am Natur 147 599–608 Occurrence Handle10.1086/285868

    Article  Google Scholar 

Download references

Acknowledgments

We thank P. Schupp for his help with field collections and for providing laboratory space at the University of Guam Marine Lab. We also acknowledge D. Gochfeld for her help with field collections, and S. Ankisetty, S. Elshahawi, and D. Burt for their assistance with secondary metabolite extractions and analyses. This work was supported by a grant from the NOAA National Institute for Undersea Technology (AGM), a University of Delaware Presidential Fellowship (CAH), and a University of Delaware Graduate Scholar’s Fellowship (CAH).

Author information

Author notes

  1. Cindi A. Hoover

    Present address: Department of Biology, Boston University, 5 Cummington St., Boston, Massachusetts, 02215, USA

Authors and Affiliations

  1. College of Marine and Earth Studies, University of Delaware, Lewes, Delaware, 19958, USA

    Cindi A. Hoover & Adam G. Marsh

  2. Department of Pharmacognosy, University of Mississippi, University, Mississippi, 38677, USA

    Marc Slattery

Authors
  1. Cindi A. Hoover
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marc Slattery
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Adam G. Marsh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cindi A. Hoover.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hoover, C.A., Slattery, M. & Marsh, A.G. Profiling Transcriptome Complexity and Secondary Metabolite Synthesis in a Benthic Soft Coral, Sinularia polydactyla . Mar Biotechnol 9, 166–178 (2007). https://doi.org/10.1007/s10126-006-6048-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-006-6048-y

Keywords

Search

Navigation