We designed probes from UCEs by including flanking sequence from medaka.Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across fishes.Get protocols » The most complex part of using UCEs to understand evolutionary relationships, population structure, and population relationships is analyzing the DNA sequence data. Mc Cormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing. Generally speaking, these commercial vendors will accept DNA extracts for enrichment, conduct the library preparation and enrichment steps, sequence the enriched libraries, and return the sequence data to you. We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting.
We have discovered (see Citations) that we can collect data from UCEs and the DNA adjacent to UCE locations (flanking DNA), and that these data are useful for reconstructing the evolutionary history and population-level relationships of many organisms. 2004) and we generally assume that UCEs must be important by the very nature of their near-universal conservation across extremely divergent taxa.Because UCEs are conserved across disparate taxa, UCEs are also That's an extremely good question, and one to which we do not entirely know the answer (Dermitzakis et al. UCEs have been associated with gene regulation (Pennachio et al. However, gene knockouts of UCE loci in mice resulted in viable, fertile offspring (Ahituv et al.Capable of demultiplexing hundreds of sequence tagged libraries at once. Get splitaake » A program for automated cleaning of fastq files from sequencing.Removes adapter contamination using scythe and trims reads for quality using sickle.Get 2,001 probe set for fish » Below are several software packages we have developed to help analyze data collected from UCE loci.
All computer code is available under a flexible open-source license (BSD).Get computer software » We compiled a list of questions you may have that go beyond the details provided above. Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. Target Capture and Massively Parallel Sequencing of Ultraconserved Elements (UCEs) for Comparative Studies at Shallow Evolutionary Time Scales. Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across amniotes.If you do not find your answer in the FAQ, please get in contact with us via twitter (@ultraconserved). Keping S, Meiklejohn KA, Faircloth BC, Glenn TC, Braun EB, Kimball RT. The evolution of peafowl and other taxa with ocelli (eyespots): A phylogenomic approach. Get 2,560 probe set for amniotes » of the primate phylogeny, and the 2,560 probes targeting 2,386 loci are a subset of this larger set of probes.We welcome all code contributions, from helping to improve the code, fix bugs, improve usability, and improve documentation, which is rather sparse, at the moment.Please contact us through twitter (@ultraconserved) if you are interested in helping and/or post an issue on github for the respective package.MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.