Ecological genetics has long sought to identify and mechanistically understand the role of specific genes in ecology and evolution (Ellegren and Sheldon 2008; Endler 1986; Gillespie 1991; Lewontin 1974). Although the genomics revolution has greatly facilitated this process, especially in genomic model systems and their close relatives (Feder and Mitchell-Olds 2003; Mitchell-Olds et al. 2007), the number of model ecological systems which have been able to gain such insights has been limited (e.g. (Abzhanov et al. 2006; Nachman et al. 2003), due to a combination of high costs, small research communities, and a need for truly integrated scientific research programs. Recent technological advances in high throughput sequencing have greatly lowered the hurdles for genomic tool development and thus facilitate the development of functional genomic insights (Ellegren 2008; Margulies et al. 2005).
Here I highlight two of my recent articles on using 454 in molecular ecology:
I. Molecular Ecology paper
If you wish to see how an ecological research program focused on a phenotype of interest can quickly move from no genetic resources to developing mechanistic understanding, using the Glanville fritillary butterfly as a proof of concept example (Vera et al. 2007). Here we publish the firust use of 454 next generation sequencing to sequence the transcriptome of a non-model species, with great success. We detail our annotation, likely extent of transcriptome coverage, and use of the 454 contigs for high quality microarray design.
A Molecular Ecology News and Views article by Han Ellegren (Molecular Ecology News and Views 17(7):1629-1631) focuses on the coming changes in ecological genetics due to next generation sequencing advances and nicely introduces our 454 transcriptome sequencing paper in Molecular Ecology (Vera et al. 2007)
II. Review paper on 454 technology
The performance and implications of next generation sequencing advances are discussed in my recent review paper (Wheat 2008), with a central focus on the 454 sequencing technology. This review covers recent advances in model genomic systems as well as representative model ecological systems with previously limited genomic resources.
This paper is written for the ecologist who knows what a microsatellite or AFLP is, but perhaps not cDNA or a contig, and is a good companion paper to the recent review on traditional EST libraries and their uses (Bouck and Vision 2007). Concepts and findings are fully discussed using the relevant terminology with their common abbreviations, which I have tried to define at a general level. 454 sequencing and its error rates are discussed, followed by a review of de novo transcriptome assemblies focused on the first successful de novo assembly which happens to be in an ecological model system (the Glanville fritillary butterfly). Particular attention is paid to the difficulties ecological geneticists are likely to encounter through reviewing relevant studies in both model and non-model systems. Various post-sequencing applications of 454 generated data are presented (e.g. microarray construction, molecular marker and candidate gene development). How to use species with genomic resources to inform study of those without is discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology.
- Abzhanov, A., W. P. Kuo, C. Hartmann, B. R. Grant, P. R. Grant, and C. J. Tabin. 2006. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 442:563-567.
- Bouck, A., and T. Vision. 2007. The molecular ecologist's guide to expressed sequence tags. Molecular Ecology 16:907-924.
- Ellegren, H. 2008. Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology 17:1629-1635.
- Ellegren, H., and B. C. Sheldon. 2008. Genetic basis of fitness differences in natural populations. Nature Reviews Genetics 452:169-175.
- Endler, J. A. 1986. Natural Selection in the Wild. Princeton Univ. Press., Princeton.
- Feder, M. E., and T. Mitchell-Olds. 2003. Evolutionary and ecological functional genomics. Nature Reviews Genetics 4:651-657.
- Gillespie, J. H. 1991. The Causes of Molecular Evolution. Oxford Univ. Press, New York.
- Lewontin, R. C. 1974. The Genetic Basis of Evolutionary Change. Columbia Univ. Press, New York.
- Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. T. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M. L. I. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. G. Yu, R. F. Begley, and J. M. Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
- Mitchell-Olds, T., J. H. Willis, and D. B. Goldstein. 2007. Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet 8:845-856.
- Nachman, M. W., H. E. Hoekstra, and S. L. D'Agostino. 2003. The genetic basis of adaptive melanism in pocket mice. Proceedings of the National Academy of Sciences of the United States of America 100:5268-5273.
- Vera, C., C. W. Wheat, J. H. Marden, and I. Hanski. 2007. Rapid transcriptome characterization for a non-model organism using massively parallel 454 pyrosequencing. Molecular Ecology in press