Abstract
Next generation sequencing technology affords new opportunities in ecological genetics. This paper addresses how an ecological genetics research program focused on a phenotype of interest can quickly move from no genetic resources to having various functional genomic tools. 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). The potential future developments in 454 sequencing are also covered. 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 issues and applications of 454 generated data are presented (e.g. database management, microarray construction, molecular marker and candidate gene development). How to use species with genomic resources to inform study of those without is also discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology.
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Acknowledgements
I would like to thank Jim Marden, Ilkka Hanski, Hans Ellegren, Tom Mitchell-Olds, Cris Vera, Heiko Vogel, Roger Butlin, Scott Edwards, Jessica Hellman, and Juan Galindo for the conversations, experience, and feedback on the ideas presented in this paper. Two anonymous reviewers also provided very insightful feedback and are thanked for their effort. Funding during the writing of this paper was supported by the Academy of Finland (grants numbers 38604 and 44887, Finnish Centre of Excellence Programme, 2006–2011) and grant EF-0412651 to J. H. Marden and I. Hanski from the US National Science Foundation.
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Wheat, C.W. Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138, 433–451 (2010). https://doi.org/10.1007/s10709-008-9326-y
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DOI: https://doi.org/10.1007/s10709-008-9326-y