RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms.
Restriction-site Associated DNA (RAD) markers are rapidly becoming a standard for SNP discovery and genotyping studies even in organisms without a sequenced reference genome. It is difficult, however, to identify genes nearby RAD markers of interest or move from SNPs identified by RAD to a high-throughput genotyping assay. Paired-end sequencing of RAD fragments can alleviate these problems by generating a set of paired sequences that can be locally assembled into high-quality contigs up to 1 kb in length. These contigs can then be used for SNP identification, homology searching, or high-throughput assay primer design. In this chapter, we offer suggestions on how to design a RAD paired-end (RAD-PE) sequencing project and the protocol for creating paired-end RAD libraries suitable for Illumina sequencers.
Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
Paul D
PD
Etter
Eric
E
Johnson
D000818:Animals; D020451:Contig Mapping; D017931:DNA Primers / Q000235:genetics; D015723:Gene Library; D005819:Genetic Markers / Q000235:genetics; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D023701:Smegmamorpha / Q000235:genetics*
D017931:DNA Primers; D005819:Genetic Markers