Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Genetica. 2010 Apr;138(4):433-51. doi: 10.1007/s10709-008-9326-y. Epub 2008 Oct 18.

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing.

Author information

  • Metapopulation Research Group, Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Viikinkaari 1, Helsinki 00014, Finland. chris.wheat@stanfordalumni.org

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.

PMID:
18931921
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Springer
    Loading ...
    Write to the Help Desk