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myBaits® UCEs – Target Capture for UltraConserved Elements

Ultraconserved Elements (UCEs) are highly conserved genomic regions which are flanked by more divergent sequences.

These key areas have been identified and exploited as ideal target capture candidates for phylogenetic research on novel and non-model species, as many genomic regions are shared across large taxonomic ranges. Sets of UCE loci have been identified for various taxonomic groups, including vertebrates and insects, and similar Conserved Orthologous Set (COS) loci have even been identified in plants. More information on the utility of UCEs for genetic research can be found at ultraconserved.org.

In addition to myBaits Custom Kits, which can include any UCE markers of choice, Arbor Biosciences offers a number of common UCE and COS panels as readily stocked kits available for immediate shipment at lower per-reaction costs. As with all myBaits kits, the UCE panels are provided as a complete solution including buffers, bait sets and blockers specific to the NGS library prep of choice along with an easy to use protocol. See the full descriptions below for currently available panels and check back often as the collection grows.

Features & Benefits

Predesigned panels
Curated and ready for immediate use
Curated targets
Thousands of ultra-conserved loci identified by leading researchers
Proven results
Ever expanding list of peer-reviewed publications
Freely accessible pipelines
Simple, user-friendly data analysis
Cost-effective
Use one bait set across multiple distantly-related taxa

Figure 1. Example alignment of a 120bp UCE locus from the Tetrapods 5K baitset compared to the region containing the top BLAST hit in genomes of chicken (Gallus gallus), human, mouse (Mus musculus), and frog (Xenopus laevis. Individual bases are colored by degree of similarity between sequences (dark = high, light = low). The central 120bp UCE region is strongly conserved across all taxa, whereas immediate flanking regions are more divergent.


An expanded version of the original HymV1 design, this set of 31,829 baits (120 mer) targets 2,590 UCE loci from the insect order Hymenoptera (ants, bees, sawflies, and wasps). The principal bait list can be downloaded from http://datadryad.org/resource/doi:10.5061/dryad.89n87. It was first described in: MG Branstetter, JT Longino, PS Ward, BC Faircloth. (2017). Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods Ecol Evol

This set of 9,898 baits (120 mer) targets 2,524 UCE loci present in Hymenoptera and 16 nuclear exons (12 genes) commonly sequenced in insects. The UCE baits are a subset of the more diverse “principal” bait set, including baits from ant genomes only. The exon baits were designed from four distantly related ant species. The UCE and exon bait lists can be downloaded from http://datadryad.org/resource/doi:10.5061/dryad.89n87. The baitset was first described in: MG Branstetter, JT Longino, PS Ward, BC Faircloth. (2017). Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods Ecol Evol

This set of 2,749 baits (120 mer) targets 1,510 UCEs from the insect order Hymenoptera (ants, bees, sawflies, and wasps). The bait list can be downloaded from ultraconserved.org. It was first described in: BC Faircloth, MG Branstetter, ND White, SG Brady. (2015.) Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol Ecol Resources

This set of 5,472 baits (120 mer) targets 5,060 UCEs from tetrapods/amniotes. The 5k probes are known to enrich ~4k loci in birds and reptiles, 2-3k loci in mammals, and up to 1k loci in amphibians. The bait list can be downloaded from ultraconserved.org. It was first described in: BC Faircloth, JE McCormack, NG Crawford, MG Harvey, RT Brumfield, TC Glenn. (2012.) Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Syst Biol

This set of 2,560 baits (120 mer) targets 2,386 UCEs from amniotes. The 2.5k probes are known to enrich ~2.2k loci in birds and reptiles and ~1k loci in mammals. These baits have not been tested extensively across all tetrapods. The bait list can be downloaded from ultraconserved.org. It was first described in: BC Faircloth, JE McCormack, NG Crawford, MG Harvey, RT Brumfield, TC Glenn. (2012) Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales. Syst Biol. This bait set has also been used for phylogeographic studies by BT Smith, MG Harvey, BC Faircloth, TC Glenn, RT Brumfield. (2013) Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales. Syst Biol

This set of 2,001 baits (120 mer) targets 500 UCEs from fish. The 0.5k Actinopterygian probes are known to enrich 300-400 loci from ray-finned fishes. The bait list can be downloaded from ultraconserved.org. It was first described in: BC Faircloth, Sorenson L, Santini F, Alfaro ME. (2013). A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). PLoS ONE

This set of 14,799 baits (120 mer) targets 1,120 UCEs from the Arachnida (spiders, mites, scorpions, harvestmen, and kin). The bait list can be downloaded here. It was first described in: BC Faircloth (2017.) Identifying Conserved Genomic Elements and Designing Universal Probe Sets To Enrich Them. Methods in Ecology and Evolution. The phylogenetic utility of this bait set was demonstrated in: J Starrett, S Derkarabetian, M Hedin, RW Bryson, JE McCormack, BC Faircloth. (2016.) High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida. Mol Ecol Resources

This set of 9,678 120mer probes targets 1,061 conserved orthologous set (COS) loci in the Compositae/Asteraceae plant family. These ~10K probes are known to enrich >700 loci across a wide range of Compositae species as well as taxa from closely-related families. The bait list can be downloaded here. It was first described in: JR Mandel, RB Dikow, VA Funk, RR Masalia, SE Staton, A Kozik, RW Michelmore, LH Rieseberg, JM Burke. 2014. A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae. Applications in Plant Sciences

Ordering Information

Catalog # Description Quantity Price Contact Us
305008 myBaits UCE Actinopterygians 0.5Kv1 8 $600 Order Now
305048 myBaits UCE Actinopterygians 0.5Kv1 48 $1920 Order Now
305096 myBaits UCE Actinopterygians 0.5Kv1 96 $2880 Order Now
305108 myBaits UCE Arachnida 1.1Kv1 8 $760 Order Now
305148 myBaits UCE Arachnida 1.1Kv1 48 $2438 Order Now
305196 myBaits UCE Arachnida 1.1Kv1 96 $3658 Order Now
305208 myBaits COS Compositae/Asteraceae 1Kv1 8 $600 Order Now
305248 myBaits COS Compositae/Asteraceae 1Kv1 48 $1920 Order Now
305296 myBaits COS Compositae/Asteraceae 1Kv1 96 $2880 Order Now
305308 myBaits UCE Hymenoptera 1.5Kv1 8 $600 Order Now
305348 myBaits UCE Hymenoptera 1.5Kv1 48 $1920 Order Now
305396 myBaits UCE Hymenoptera 1.5Kv1 96 $2880 Order Now
305408 myBaits UCE Hymenoptera 2.5Kv2 Principal/Full 8 $600 Order Now
305448 myBaits UCE Hymenoptera 2.5Kv2 Principal/Ful 48 $1920 Order Now
305496 myBaits UCE Hymenoptera 2.5Kv2 Principal/Ful 96 $2880 Order Now
305508 myBaits UCE Hymenoptera 2.5Kv2 Ant-Specific 8 $600 Order Now
305548 myBaits UCE Hymenoptera 2.5Kv2 Ant-Specific 48 $1920 Order Now
305596 myBaits UCE Hymenoptera 2.5Kv2 Ant-Specific 96 $2880 Order Now
305608 myBaits UCE Tetrapods 2.5Kv1 8 $600 Order Now
305648 myBaits UCE Tetrapods 2.5Kv1 48 $1920 Order Now
305696 myBaits UCE Tetrapods 2.5Kv1 96 $2880 Order Now
305708 myBaits UCE Tetrapods 5Kv1 8 $600 Order Now
305748 myBaits UCE Tetrapods 5Kv1 48 $1920 Order Now
305796 myBaits UCE Tetrapods 5Kv1 96 $2880 Order Now

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