myBaits Custom — Predesigned Community Panels
Animals
NGS Community Panels for animals.

Over the last decade, researchers working in evolutionary biology, phylogenetics, functional genomics, environmental and community genomics, and more have relied on myBaits Custom kits for enhancing the efficiency of their targeted next-generation sequencing (NGS) research on a wide variety of model and non-model animal species.

myBaits Custom kits have been applied to NGS research for virtually all animal phyla including arthropods, chordates, cnidaria, echinoderms, molluscs, and more. Vertebrate research has been heavily represented for both extant and extinct taxa, including tetrapods and Chrondrichtyhes and Osteichthyes fishes.



Overview

myBaits Custom Community Panels for Animals

Listed below are a curated set of animal research panels that are of broad interest to the research community, and are available for quick delivery. Daicel Arbor Biosciences extends our thanks to the authors and designers of these panels for granting permission to include them on this list for accelerating discovery of the research community.

Note about attribution: If you use one of these Community Panels (in full or modified form) in your research, please ensure that you properly cite the appropriate publication(s) in any resulting manuscripts. Where applicable, we have indicated the most appropriate current reference(s) that should be cited for each panel.

Animals

FrogCap - Ranoidea V1

Enrichment panel designed for Ranoidea frog phylogenetics that includes exon markers plus legacy and UCE markers for a total of >13.5K markers targeting >3.4 Mbp. Exon marker sequences derive from the Nanorana parkeri reference genome. Hutter et al. (2021) evaluated the panel and demonstrated its effectiveness on a range of samples within the Ranoidea superfamily. More info at frogcap.com.

Reference: Hutter, C.R., K.A. Cobb, D.M. Portik, S.L. Travers, P.L. Wood, R.M. Brown. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22: 1100–1119.

Design ID: D10259HFrog

FrogCap - Ranoidea V2

Enrichment panel designed for Ranoidea frog phylogenetics that is a revised version of the Ranoidea V1 panel described above; the final design targets >3.3 Mb and includes >10.7K exon markers, >2K UCEs, and 86 additional legacy markers (Hutter et al 2021). More info at frogcap.com.

Reference: Hutter, C.R., K.A. Cobb, D.M. Portik, S.L. Travers, P.L. Wood, R.M. Brown. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22: 1100–1119.

Design ID: D10260HFRn2

FrogCap - Hyloidea V1

Enrichment panel designed for Hyloidea frog phylogenetics that includes transcript markers plus legacy and UCE markers for a total of >9K markers targeting >2.9 Mbp. Transcriptome markers derive from six Hyloidea species transcriptome datasets. Hutter et al. (2021) evaluated the panel and demonstrated its effectiveness on a range of samples within the Hyloidea superfamily. More info at frogcap.com.

Reference: Hutter, C.R., K.A. Cobb, D.M. Portik, S.L. Travers, P.L. Wood, R.M. Brown. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22: 1100–1119.

Design ID: D10257HFHy1

FrogCap - Hyloidea V2

Enrichment panel designed for Hyloidea frog phylogenetics that is a revised version of the Hyloidea V1 panel described above; the final design targets >3 Mbp and includes >8.5K exon markers, >2K UCEs, and 86 additional legacy markers (Hutter et al 2021). More info at frogcap.com.

Reference: Hutter, C.R., K.A. Cobb, D.M. Portik, S.L. Travers, P.L. Wood, R.M. Brown. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22: 1100–1119.

Design ID: D10261HFHy2

FrogCap - Reduced (Ranoidea)

Enrichment panel designed for Ranoidea frog phylogenetics that is a scaled-down version of the Ranoidea V1 panel described above; the final design targets >3K markers from the Ranoidea V1 set plus another 86 additional legacy markers. Hutter et al (2021) evaluated the panel and demonstrated its effectiveness in samples from genus Occidozyga. More info at frogcap.com.

Reference: Hutter, C.R., K.A. Cobb, D.M. Portik, S.L. Travers, P.L. Wood, R.M. Brown. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources, 22: 1100–1119.

Design ID: D10255HFRn1

PaleoChip Arctic-1.0 Animal - Mitochondrial genome panel for eDNA

Enrichment panel designed for capturing animal mitochondrial DNA from environmental ancient DNA (‘sedaDNA’) samples. Approximately 180 taxa were used for bait design, primarily megafauna of extinct/extant Quaternary animals. Murchie et al (2020) designed the panel and demonstrated its effectiveness on sedaDNA samples, pooled in a 5:3 ratio (Animal:Plant; total baits/rxn = 200ng) with the separate “Plant” PaleoChip Arctic-1.0″ baitset, which is also available as a Community Panel from Daicel Arbor Biosciences.

Reference: Murchie, T.J., M. Kuch, A.T. Duggan, M.L. Ledger, K. Roche, J. Klunk, E. Karpinski, D. Hackenberger, T. Sadoway, R. MacPhee, D. Froese, H. Poinar. (2021). Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set. Quaternary Research, 99:305–328.

Design ID: D10185eANML

MegaMito - Mitochondrial genome panel for eDNA

Enrichment panel designed for full mitochondrial DNA (mtDNA) genome capture from ancient DNA samples. First published and demonstrated effective in Kirillova et al (2017). Baits designed from 75 mammalian target sequences to work even for highly degraded aDNA target molecules. Target sequences include species from Artiodactyla, Carnivora, Eulipotyphla, Lagomorpha, Perissodactyla, Pholidota, Primates, Proboscidea, Rodentia, Tubulidentata, and Xenarthra.

Reference: Kirillova, I.V., O.F. Chernova, J. van der Made, V.V. Kukarskih, B. Shapiro, J. van der Plicht, F.K. Shidlovskiy, P.D. Heintzman, T. van Kolfschoten, O.G. Zanina. (2017). Discovery of the skull of Stephanorhinus kirchbergensis (Jäger, 1839) above the Arctic Circle. Quaternary Research, 88:537–550.

Design ID: D10361MgMT

Anthozoa-V1

Enrichment panel designed for phylogenetics in anthozoa (stony corals, soft corals, and anemones). Quattrini et al (2018) designed the panel of >16K probes targeting 720 UCEs and 1,071 exon loci and demonstrated it effective across 33 samples representing all Anthozoa orders, recovering on average 638 loci per species.

Reference: Quattrini, A.M., B.C. Faircloth, BC, L.F. Dueñas, T.C.L. Bridge, M.R. Brugler, I.F. Calixto-Botía, D.M. DeLeo, S. Forêt, S. Herrera, S.M.Y. Lee, D.J. Miller, C. Prada, G. Rádis-Baptista, C. Ramírez-Portilla, J.A. Sánchez, E. Rodríguez, C.S. McFadden. 2018. Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems. Molecular Ecology Resources; 18: 281– 295.

Design ID: D10349ANTHZ

Octocoral-V2

Enrichment panel designed for octocorals targeting 3,023 loci (1,337 UCE and 1,686 exons), a.k.a. octo-v2. Redesigned expanded version of anthozoa-v1 optimized for octocorals. Erickson et al (2021) designed this baitset and demonstrated it to be effective via testing with samples representing two octocoral genera, Alcyonium and Sinularia; on average >1,900 loci were recovered per sample.

Reference: Erickson, K.L., A. Pentico, A.M. Quattrini, C.S. McFadden. (2021). New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons. Molecular Ecology Resources 2021; 21: 78– 92.

Design ID: D10150Oc219

Hexacoral-V2-Scleractinia

Enrichment panel designed for Hexacorallia stony corals targeting 2,476 loci (1,436 UCE and 1,040 exons), a.k.a. hexa-v2-scleractinia. Redesigned expanded version of anthozoa-v1 baitset optimized for hexacorals. Cowman et al (2020) designed this baitset and demonstrated it to be effective via testing with 99 samples representing scleractinian corals from Acroporidae, Agariciidae, and Fungiidae; on average >1,800 loci recovered for each taxon resulting in total aligned dataset of >1.8 Mbp.

Reference: Cowman, P.F., A.M. Quattrini, T.C.L. Bridge, G.J. Watkins-Colwell, N. Fadli, M. Grinblat, T.E. Roberts, C.S. McFadden, D.J. Miller, A.H. Baird. (2020). An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Molecular Phylogenetics and Evolution 153: 106944.

Design ID: D10350PCCRL

Hexacoral-V2-Actiniaria

Enrichment panel designed for antiniarian corals targeting 2,496 UCE and exon loci, a.k.a. hexa-v2-actiniaria. Redesigned version of anthozoa-v1 baitset optimized for actiniarian corals. Erickson et al (2021) designed this baitset and demonstrated it to be effective for species-level resolution with the sea anemone genus Metridium. The bait capture approach provided greater support for both species and geographic differentiation compared to both ddRAD data and nuclear/mito systematics amplicon markers.

Reference: Glon, H., A. Quattrini, E. Rodríguez, B.M. Titus, M. Daly. (2021). Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans. Molecular Phylogenetics and Evolution 163: 107233.

Design ID: D10352HxV2A

Note about attribution: If you use one of these Community Panels (in full or modified form) in your research, please ensure that you properly cite the appropriate publication(s) in any resulting manuscripts. Where applicable, we have indicated the most appropriate current reference(s) that should be cited for each panel.

To order, please reach out to our team today to get started quickly with one of these demonstrated peer-reviewed options.

Have a suggestion to add a new panel to our list? Contact us today!

Daicel Arbor Biosciences offers both custom probes and full NGS services to meet your project needs. If you do not see a suitable option among these or our predesigned myBaits Expert panels, our scientists would be happy to design a fully custom targeted NGS panel and kit that will exactly meet your research needs. Please contact us today, and visit our myBaits Custom DNA-Seq, myBaits Custom RNA-Seq, or myBaits Custom Methyl-Seq product pages to learn more. And if you’d like to outsource your targeted NGS project, our myReads lab services experts are always available to perform library preparations, target capture, sequencing, and analysis for any application.

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All myBaits kits are for research-use only, and are not validated for diagnostic or therapeutic purposes.

Services

End-to-End Solutions for Your Next NGS Project

Daicel Arbor Biosciences operates a full-services NGS laboratory that can handle any scale project for custom targeted sequencing or whole genome or whole transcriptome sequencing. We have processed thousands of DNA and RNA samples with an extremely high success rate, even for difficult and challenging samples. We can develop a new custom kit specifically tuned to your exact research targets of interest, or utilize one of our recommended predesigned baitsets for rapid processing.

In addition, our in-house team can now work directly with you to provide cloud-based and bespoke bioinformatics solutions. With years of NGS experience across a wide variety of applications, we can develop a custom solution to fit your expertise and research needs.

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Publications

Featured Publications

The featured publications listed below correspond to the collection of Community Panels highlighted in the Overview tab. For hundreds more examples of published papers that utilize myBaits Custom and Expert kits, please visit our dedicated Publications page. Daicel Arbor Biosciences thanks these authors for sharing their probe designs for the benefit of the wider research community!

Note about attribution: If you use one of these Community Panels (in full or modified form) in your research, please ensure that you properly cite the appropriate publication(s) in any resulting manuscripts. Where applicable, we have indicated the most appropriate current reference(s) that should be cited for each panel.

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