We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Comparative performance of double-digest RAD sequencing across divergent arachnid lineages.
- Authors
Burns, Mercedes; Starrett, James; Derkarabetian, Shahan; Richart, Casey H.; Cabrero, Allan; Hedin, Marshal
- Abstract
Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease ( RE) selection in double-digest restriction-site-associated DNA sequencing (dd RADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the py RAD program. The 6-base pair cutter Eco RI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for dd RADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.
- Subjects
NUCLEOTIDE sequencing; DNA restriction enzymes; ARACHNIDA; LINEAGE; OPILIONES
- Publication
Molecular Ecology Resources, 2017, Vol 17, Issue 3, p418
- ISSN
1755-098X
- Publication type
Article
- DOI
10.1111/1755-0998.12575