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Coral Genomics

General Genomics Information Sources

Genomics for Non-Genomic ScientistsCourse: ‘Genomics for Non-Genomic Scientists’ June 21-27, 2009 presented at the USFWS National Conservation Training Center, Shepherdstown, WV; sponsored by NOAA & NCRI.

A week-long introductory course was presented to 20 non-genomic scientists interested in learning the basics of genomics terminology and tools for the study of corals. The hands-on, problem-solving oriented course was organized and team taught by (shown in the photo from left to right) Drs. Cheryl Woodley, Shini Sunagawa (Univ. CA Merced), Joe Lopez (NOVA Southeastern Univ.), Monica Medina (Univ. CA Merced), Monica Munoz-Torres (Georgetown Univ), Kurt Kwast (Univ. IL) and Shawn Polson (Univ. DE). Lectures were video recorded and are being made available along with slide presentations. The course instructors compiled a comprehensive reference list that also is provided below. The participants took a short survey before and after completing the course to assess the focus and level of learning accomplished during the week.

  • Course InstructorsCourse Outline
    • Introduction to Genomics
    • Sequence Data
    • Eukaryotic Annotation
    • Transcriptomics
    • EST2uni Lab
    • Single Gene Analysis
    • 16S RNA Analysis
    • RDP Lab: LibCompare, SeqMatch, Classifier
    • 16S Lab – R and other Comparison Tools
    • Metagenomics
    • Metagenomic Analysis
    • Microarrays (not all chips are created equal)
    • Microarray analysis, Nuts and bolts of (hands on analysis)
    • Capstone
  • Supporting Information
    • Slide Presentations
      • NCBI Tutorial, M. Munoz-Torres (pdf, 2.9 Mb)
      • 16S RNA Analysis, S. Sunagawa (pdf, 5.8 Mb)
      • Beyond 16S, S. Polson (pdf, 1.9 Mb)
      • 16S Lab, S. Polson (pdf, 2.1 Mb)
      • Introduction to Genomics Databases, J. Lopez (pdf, 47.6 Mb)
      • DNA Microarrays, K. Kwast (pdf, 8.8 Mb)
      • Capstone, K. Kwast (pdf, 1.0 Mb)
    • Video Lectures, Genomics Workshop
      • Lecture 01, Introduction to Genomics, Monica Medina (swf, 430 Kb)
      • Lecture 02, Introduction to Genomics cont’, Monica Medina (swf, 433 Kb)
      • Lecture 03, Introduction to Genomics cont’, Monica Medina (swf, 432 Kb)
      • Lecture 04, Introduction to Genomics cont’, Monica Medina (swf, 436 Kb)
      • Lecture 05, Sequence databases, Monica Munoz-Torres; Genome Annotation, Monica Medina (swf, 436 Kb)
      • Lecture 06, Genome Annotation cont’, Monica Medina; Arabidopsis genome database & genome communities, Monica Munoz-Torres; Transcriptomics, Joe Lopez (swf, 435 Kb)
      • Lecture 07, Methods for study of transcriptomics, Joe Lopez; EST databases, Shini Sunagawa (swf, 429 Kb)
      • Lecture 08, Working with ESTs, using ET2Uni, Shini Sunagawa (swf, 435 Kb)
      • Lecture 09, Using EST data to answer questions, Shini Sunagawa; Bacterial rDNA tools, Joe Lopez; Microbial ecology tools & phylogenetics of microbes, Shini Sunagawa (swf, 432 Kb)
      • Lecture 10, Microbial ecology tools cont’, Shini Sunagawa; Summary of microbial ecology tools & 16S ribosomal genes, Shawn Polson (swf, 428 Kb)
      • Lecture 11, 16S ribosomal DNA pros & cons, data mining, metagenomics, Shawn Polson (swf, 435 Kb)
      • Lecture 12, Metagenomic analysis cont’, Shawn Polson (swf, 428 Kb)
      • Lecture 13, Microarrays, Kurt Kwast (swf, 430 Kb)
      • Lecture 14, Running microarrays, Kurt Kwast (swf, 418 Kb)
      • Lecture 15, Microarray experiments, Kurt Kwast (swf, 430 Kb)
      • Lecture 16, Practice microarray dataset, Kurt Kwast; Capstone - coral genome now & future, Monica Medina; Organellar genomes – mitochondria, Joe Lopez (swf, 427 Kb)
    • Self-Assessment Tool, (pdf, xxMb)
  • Recommended Reading Lists
    • Recommended Course Text:
      • A Primer of Genome Science, Third Edition Greg Gibson and Spencer V. Muse http://www.sinauer.com/detail.php?id=2368#purchase
    • Medina Reading List
      • Jodi A Schwarz, Peter B Brokstein, Christian Voolstra, Astrid Y Terry, David J Miller, Alina M Szmant, Mary Alice Coffroth and Mónica Medina. 2008. Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics. 9:97
      • O. Levy, et al. 2007. Light-Responsive Cryptochromes from a Simple Multicellular Animal, the Coral Acropora millepora. Science. 318: 467.
    • Lopez Reading List Transcriptome
      • DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503
      • DeSalvo MK, Voolstra CR, Sunagawa S, Schwarz JA, Stillman JH, Coffroth MA, Szmant AM, Medina M. 2008. Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata. Mol Ecol. 17(17):3952-71. Epub 2008 Jul 24.
      • Edge, S.E. et al 2005. Development of a coral cDNA array to examine gene expression profiles in Montastraea faveolata exposed to environmental stress. Mar Pollut Bull., 51:507-23.
      • Gracey, A.Y. 2007. Interpreting physiological responses to environmental change through gene expression profiling. J Exp Biol., 210(Pt 9):1584-9. ? Grasso LC, Maindonald J, Rudd S, Hayward DC, Saint R, Miller DJ, Ball EE. 2008. BMC Genomics. 9:540.
      • Meyer E. et al. 2009. Sequencing and de novo analysis of coral larval transcriptome by 454 GS-FIX. BMC Genomics 2009, 10:219. PDF
      • Rodriguez-Lanetty M. et al. 2006. Transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression. BMC Genomics 7:23.
      • Wang, S. et al. 2009. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). J. Hered. 100, 329-337. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I 2008.
      • Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE. 2008 Aug 22;3(8):e3042.

        Workbench, Fastgroup II and other relevant microbial community analyses
      • Cassler, M., Winegar, R. , McCarthy, P.J., Pomponi, S.A., Peterson, C.L, Wright, A.E, Lopez, J.V. 2008. Use of Real-Time PCR to quantitate the unculturable heterotrophic bacterial community in deep sea marine sponges of the family Lithistidae. Microbial Ecology 55:384-394. PDF
      • Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F. 2008. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE. 2008 Feb 27; 3(2):e1584. PDF ? Gunasekera, A., Sfanos, K.A, McCarthy, P.J., Lopez, J.V. 2005. HBMMD: an enhanced database of the microorganisms associated with deeper water marine invertebrates. Applied Microbiol. Biotechnol. 66(4):373-376.
      • Rubin E.T., Lopez, J.V., Gilliam, D.S., Dodge, R.E., Kosmynin, V.N., Moulding, A.L. Scleractinian coral recruitment patterns to reefs Physically damaged by ship groundings. Proc 11th ICRS. In Press.
      • Sfanos, K.A.S., Harmody, D.K., McCarthy, P.J., Dang, P., Pomponi, S.A. and Lopez, J.V. 2005. A Molecular Systematic Survey of Cultured Microbial Associates of Deep Water Marine Invertebrates. System Appl Microbiol. 28 (3):242-264. PDF
      • Subramaniam S. The Biology Workbench: A seamless database and analysis environment for the biologist. Proteins.1998; 32: 1-2.
      • Yu, Y. et al. 2006. FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries, BMC Bioinformatics 2006,7:57
    • Sunagawa Reading List
          EST databases
          Background
       
      • A hitchhiker's guide to expressed sequence tag (EST) analysis - Nagaraj et al., Briefings in Bioinformatics 2007, 8(1):6-21
      • Genomics of Basal Metazoans - Steele, R., Integrative and Comparative Biology 2005 45(4):639-648.

        Relevant to exercises
      • EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration - Forment et al., BMC Bioinformatics 2008, 9:5.
      • Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation - Kondrashov et al., Biology Direct 2006, 1:31.

        Dataset publications
      • Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx - Meyer et al., BMC Genomics 2009, 10:219.
      • Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont - Sunagawa et al., 2009, BMC Genomics 2009, 10:258.
      • Schwarz, J. A., P. B. Brokstein, C. Voolstra, A. Y. Terry, A. Szmant, M. A. Coffroth, D. J. Miller, and M. Medina (2008). Coral Life History and Symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata. BMC Genomics 9: 97.
      • Voolstra, C.R., S. Sunagawa, J. A. Schwarz, M.A. Coffroth, D. Yellowlees, W. Leggat, M. Medina (2009). Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comp Biochem Physiol D: doi:10.1016/j.cbd.2008.11.001.
      • Leggat, W., Hoegh-Guldberg, O., Dove, S., Yellowlees, D. Analysis of an EST library from the dinoflagellate (Symbiodinium sp.) symbiont of reef-building corals. Journal of Phycology, 2007.

        Tools
      • Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
      • Contreras-Moreira, B., Sachman-Ruiz, B., Figueroa-Palacios, I., and Vinuesa, P. (2009). primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucl. Acids Res., doi:10.1093/nar/gkp377.

        Ribosomal Database Project

        Reference dataset
      • Sunagawa, S., T.Z. DeSantis, Y.M. Piceno, E.L. Brodie, M.K. DeSalvo, C.R. Voolstra, E. Weil, G.L. Andersen, M. Medina. Bacterial Diversity and White Plague Disease-Associated Community Changes in the Caribbean Coral Montastraea faveolata. The ISME Journal 3, 512-521, 2009. PDF

        Highly recommended
      • Video tutorials on RDP website: http://rdp.cme.msu.edu/help/tutorial.jsp

        Background
      • Denner EBM, Smith GW, Busse HJ, Schumann P, Narzt T, Polson SW et al. (2003). Aurantimonas coralicida gen. nov., sp nov., the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol 53: 1115–1122.
      • Richardson LL, Goldberg WM, Kuta KG, Aronson RB, Smith GW, Ritchie KB et al. (1998b). Florida’s mystery coral-killer identified. Nature 392: 557–558.
    • Polson’s Reading List
      • Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, et al. 2008 Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS ONE 3(2): e1584. doi:10.1371/journal.pone.0001584
      • Handelsman, Jo. Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiol. Mol. Biol. Rev. 2004 68: 669-685
      • F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386doi:10.1186/1471-2105-9-386
      • Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev. 2009 Jan;33(1):109-32. Epub 2008 Nov 24.