Reducing Sequence Capture Costs with Universal Library Preparation Methods (Adapterama) and Ultraconserved Element (UCE) Bait Sets

Sequence capture is an efficient way to survey many loci simultaneously, but expenses and other limitations associated with library preparation and bait development constrain the application of sequence capture more generally. We have developed a general approach for Illumina library preparations (Adapterama) to create libraries that are functionally equivalent to and poolable with dual-indexed Illumina TruSeq libraries. Adapterama uses sets of universal primers to reduce costs associated with: 1) start-up (i.e., doing NGS for the first time), 2) buy-in (i.e., getting any data from a run), and 3) sample preparation. Adapterama allows more than 74,000 primer combinations, a number far greater than typically needed within an Illumina run, allowing multiple users and projects to have their own unique sets of indexes, facilitating the sharing of runs among users and projects. We have used the Adapterama approach to create libraries via random shearing and restriction enzymes (RADseq) which have been used to reduce costs for sequence capture. To address the constraint of bait development, we have developed baits to ultraconserved elements (UCEs). Each of the UCE bait sets recovers thousands of orthologous loci for tens of thousands of species. UCE loci are useful for studies ranging from mating systems to phylogeography to deep phylogenetics. Several fully validated UCE bait sets are available as low-cost catalog items from Mycroarray, with more on the way. New tools for more researchers to create their own sets of UCE loci are now available.