Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development

Molecular Ecology Resources - Tập 11 Số 6 - Trang 1093-1101 - 2011
M. Gardner1,2,3, Alison Fitch3, Terry Bertozzi4, Andrew J. Lowe1,2
1Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, North Terrace, Adelaide, SA 5001, Australia
2Department for Environment and Heritage, State Herbarium, Science Resource Centre, Adelaide, SA 5005, Australia
3School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
4Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia

Tóm tắt

AbstractNext generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large‐scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.

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Molecular Ecology Resources

Tập 11 Số 6

1093-1101

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