SBG/ddRAD-SEQ
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WHAT IS SBG/ddRAD SEQUENCING?
Sequence-based genotyping (SBG), also known as double digest RAD Sequencing (ddRAD-Seq) is a genomic sequencing technique that also sequences the same subset of a genome across a large number of samples at one time. SBG / ddRAD-Seq uses two restriction enzymes - one a frequent cutter and the other an infrequent cutter. The infrequent cutter anchors the fragments on the 5’ end, while the frequent cutter reduces the number of fragments sequenced. Our licensed SBG / ddRAD-Seq protocol makes use of optional selective primers during final amplification, which can further reduce the number of fragments sequenced making this a highly tunable solution for larger genomes (>5Gbp).
APPLICATIONS
Like RAD-Seq, SBG can be useful for population genetics, phylogenetics and conservation studies, and is best applied when fewer sites than a standard RAD project are needed. Additionally, SBG’s flexibility is well suited to species with large genomes (>5Gbp) that need deep coverage per site or where sample inputs are limited like small insects or extremely limited tissue samples. Some common applications include:
Projects with large genomes (>5Gbp up to 30+Gbp) and many restriction sites
Projects where DNA is precious and/or limited
Plant & animal breeding
Marker-trait association
EXAMPLE SBG/ddRAD-SEQ PROJECT
Low Concentration Inputs
Surveyed 380 small insect samples with average concentration of 7 ng/ul vs 20 ng/ul required input DNA
Used enzymes PstI and MseI to fragment genome
Generated 1.9M 1x100 bp Illumina Reads per sample
Identified 3.6K SNPs for population structure analysis
Large Genomes
Processed 180 amphibian samples, genome size >30 Gbp
Used enzymes PstI and MseI to fragment genome, with further reduction of loci with selective primers
Generated 4M 1x100 bp Illumina reads per sample