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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.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.
Frequently asked questions » Faircloth BC, Branstetter MG, White ND, Brady SG. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. All probes are available under a CC0 license, thus freely available for you to use, without restriction.
You can identify UCEs in organismal genome sequences by aligning several genomes to each other, scanning the resulting genome alignments for areas of very high (95-100%) sequence conservation, and filtering on user-defined criteria, such as length (e.g., Bejerano et al. If you want to use these regions as genetic markers, it is best to remove UCEs that appear to be duplicates of one another which we loosely define as being in more than one spot within each genome that you aligned.
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.
Once we design a probe set, we follow sequence capture protocols to enrich DNA libraries for the target UCEs, usually in multiplex. Faircloth BC, Mc Cormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. These talks should give a general idea of where we're going with new research projects that use UCEs.