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The resulting loci are the highly conserved that we target for use as molecular markers. 2009) probes that are similar in sequence to the UCE loci we are targeting. Here's a list of UCE-related talks at various conferences.
These probe sets differ in number and composition, depending on the types of questions we are asking and the taxa with which we are working. Mc Cormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. Ultraconserved Elements Are Novel Phylogenomic Markers that Resolve Placental Mammal Phylogeny when Combined with Species Tree Analysis. Slides are available for each talk by clicking on the linked talk title.
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.
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 created several software packages and we're working on tutorials to help get you started. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). We do not derive any referall revenue from these companies, but we list each here to help interested labs get started. We have several larger probes sets in the works, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. You can now buy each of these probe sets direct from MYcroarray in the form of a capture kit.
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.
Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across fishes.
Many of the steps, at this point, require that you are comfortable working with computer software on the command line. MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
We encourage everyone interested to get the software and contribute to the effort of documenting, improving, and extending our computer code. Order enrichment kits from MYcroarray » We designed probes from UCEs by including flanking sequence from chickens.
Concatenates reads into an "interleaved" file for use with velvet.
Report an issue with illumiprocessor Get illumiprocessor » A program started by Nick Crawford with contributions from Brant Faircloth for parallel computation of individual genetrees and the estimation of a species tree from gene tree data.