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Targeted DNA Region Re-sequencing

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Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

Abstract

Although massively parallel sequencing (MPS) allows researchers to obtain huge amounts of data at low cost compared to Sanger sequencing, current costs and computational constraints for whole genome sequencing and analysis generally prohibit phylogenomic and population genomic studies of non-model organisms and species with large, complex genomes. Therefore, new methods have been developed to select specific genomic regions for re-sequencing. Many of these methods can be applied to non-model organisms or species with very few genetic resources. Choosing which method to use for the study system of interest often depends on a variety of factors. In this chapter, we describe various re-sequencing methods with a focus on target enrichment. Additionally, we lay out experimental design considerations, bioinformatics pipelines, and proper reporting of results for target enrichment.

Karolina Heyduk and Jessica D. Stephens are contributed equally with all other contributors.

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    Authors and Affiliations

    1. Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA

      Karolina Heyduk & Jessica D. Stephens

    2. Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA, 70803, USA

      Brant C. Faircloth

    3. Department of Environmental Health Science, University of Georgia, 150 East Green St, Athens, GA, 30602, USA

      Travis C. Glenn

    Authors
    1. Karolina Heyduk
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    2. Jessica D. Stephens
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    3. Brant C. Faircloth
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    4. Travis C. Glenn
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    Correspondence to Travis C. Glenn .

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    Editors and Affiliations

    1. Genome Analysis Platform, CIC bioGUNE, Derio, Spain

      Ana M. Aransay

    2. Genome Analysis Platform, CIC bioGUNE, Derio, Spain

      José Luis Lavín Trueba

    Annex: Quick Reference Guide

    Annex: Quick Reference Guide

    Fig. QG3.1
    figure a

    Representation of the wet-lab procedure workflow

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    Fig. QG3.2
    figure b

    Main steps of the computational analysis pipeline

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    Table QG3.1 Experimental design considerations
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    Table QG3.2 Available software recommendations
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    Heyduk, K., Stephens, J.D., Faircloth, B.C., Glenn, T.C. (2016). Targeted DNA Region Re-sequencing. In: Aransay, A., Lavín Trueba, J. (eds) Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer, Cham. https://doi.org/10.1007/978-3-319-31350-4_3

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