Chapter

Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

pp 43-68

Date:

Targeted DNA Region Re-sequencing

  • Karolina HeydukAffiliated withDepartment of Plant Biology, University of Georgia 
  • , Jessica D. StephensAffiliated withDepartment of Plant Biology, University of Georgia 
  • , Brant C. FairclothAffiliated withDepartment of Biological Sciences and Museum of Natural Science, Louisiana State University
  • , Travis C. GlennAffiliated withDepartment of Environmental Health Science, University of Georgia Email author 

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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.

Keywords

Phylogenomics Population genomics Target enrichment