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.
Removes adapter contamination using scythe and trims reads for quality using sickle.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.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.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.
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.
Following enrichment, we sequence the DNA enriched for UCEs using massively parallel sequencing. Crawford NG, Faircloth BC, Mc Cormack JE, Brumfield RT, Winker K, Glenn TC. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Go to talks » Below are several commercial laboratories offering UCE enrichment as a service.
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.
As their name implies, ultraconserved elements (UCEs) are highly conserved regions of organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs with humans.