What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci?

Question

The article about "rapture sequencing" found here says:

"This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed."

My question is regarding the second sentence. What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci? How do the RAD tags target sequencing reads, if that is what is being said here? How does this relate to combining the benefits of both reduced representation sequencing techniques, or am I missing the crux of the paper?

Answer 1

This method is essentially combining the techniques of RAD sequencing with targeted sequence capture. Both are reduced-representation DNA sequencing techniques, meaning that instead of sequencing all the DNA from a sample, only a portion of the DNA is sequenced. The main advantage is for studies that don't require a completely sequenced genome for every sample, allowing reduced sequencing for many samples and more effectively using limited sequencing capacity.

RAD sequencing reduces the sample genome essentially randomly, though the selection should be similar for closely-related individuals (it's based on the locations of restriction enzyme sites). Targeted sequence capture allows for specific genes or genomic locations to be sequenced, discarding the rest, but this requires some prior knowledge of the locations of interest (it anneals complimentary nucleotides to the region, similar to how PCR primers work).

This method first performs the "random" reduction of RAD, and then from those fragments captures the loci of interest (500 in the referenced article).

The authors claim this makes for easier library prep and cleaner results.