hyRAD
Hybridization RAD for Degraded DNA
hyRAD (Suchan et al., 2016) was developed for use on degraded DNA samples, such as those from museum collections. Museum and preserved samples offer a rich source of valuable specimens, but their degraded DNA is unable to sustain the double-digestion and sample fractionation required by ddRAD (Peterson et al., 2012). To address this limitation, hyRAD uses biotinylated probes and streptavidin-covered beads to capture and enrich the fragments of interest.
The first step in the process is to generate a ddRAD library from high-quality DNA, usually from an extant specimen. The fragments are size-selected and biotinylated. They can now be used as probes for hybridization capture of shotgun or ddRad libraries.
Advantages:
- Can be used on degraded DNA
- Can be used on unsequenced genomes
Disadvantages:
- Coverage not as complete as with high-quality samples
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;
Holmes M. W., Hammond T. T., Wogan G. O., et al. Natural history collections as windows on evolutionary processes. Mol Ecol. 2016;25:864-881
References:
Suchan T., Pitteloud C., Gerasimova N. S., et al. Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens. PLoS One. 2016;11:e0151651
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History: hyRAD
Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
Hybridization RAD for Degraded DNA
hyRAD (Suchan et al., 2016) was developed for use on degraded DNA samples, such as those from museum collections. Museum and preserved samples offer a rich source of valuable specimens, but their degraded DNA is unable to sustain the double-digestion and sample fractionation required by ddRAD (Peterson et al., 2012). To address this limitation, hyRAD uses biotinylated probes and streptavidin-covered beads to capture and enrich the fragments of interest.
The first step in the process is to generate a ddRAD library from high-quality DNA, usually from an extant specimen. The fragments are size-selected and biotinylated. They can now be used as probes for hybridization capture of shotgun or ddRad libraries.
Advantages:- Can be used on degraded DNA
- Can be used on unsequenced genomes
Disadvantages:- Coverage not as complete as with high-quality samples
Reagents:Illumina Library prep and Array Kit SelectorReviews:Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;Holmes M. W., Hammond T. T., Wogan G. O., et al. Natural history collections as windows on evolutionary processes. Mol Ecol. 2016;25:864-881References:Suchan T., Pitteloud C., Gerasimova N. S., et al. Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens. PLoS One. 2016;11:e0151651