myBaits Custom — Predesigned Community Panels
Plants and Fungi
NGS Community Panels for plants and fungi.

myBaits Custom — Predesigned Community Panels – Plants and Fungi

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 plant and fungal targeted next-generation sequencing (NGS) research.

For plants, all major land plant groups including non-vascular and vascular plants have been studied using myBaits Custom panels, including all major seed plant groups. Other major eukaryotic taxonomic groups such as algae and fungi have also been studied using myBaits.



Overview

myBaits Custom Community Panels for Plants and Fungi

Listed below are a curated set of plant and fungal 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.

Plants

Wheat Promoters - Wheat regulatory elements panel

Large next-generation sequencing enrichment panel demonstrated to broadly and efficiently enrich regulatory element genomic regions from wheat and related species. Targets ~168 Mbp genome space of IWGSC RefSeq v1.0 genome. Tests on hexaploid, tetraploid, and diploid wheat samples exhibited excellent target coverage with improved specificity/sensitivity compared to a legacy probeset from another manufacturer. Captures from a Kronos TILLING population detected avg >3K EMS-induced mutations per line. See poster virtually presented at the 2022 PAG meeting for more details.

Reference: Zhang, J., G. Burguener, J. Debernardi, F. Choulet, E. Paux, J. Enk, J. Dubcovsky. (2022). Comprehensive and cost-effective genomic regulatory element sequencing for wheat. Poster presented at the International Plant and Animal Genomes meeting (PAG XXIX), January 2022.

Design ID: D10107WtPrm

Wheat Genotyping - 15K

Enrichment panel targeting ~15K genotyping SNP markers in hexaploid wheat (Triticum aestivum). Burridge et al (2017) designed the panel based on existing wheat GBS marker sets to maximize comparative utility across different genotyping-by-sequencing platforms. Total panel targets >15K markers (1 probe per allele = ~30K total probes), all of which were known to be polymorphic in UK wheat populations and had defined chromosomal locations. Experiments by Burridge et al (2017) demonstrated strong capture performance and revealed a focused subset of 3,256 markers identified to have maximum signal congruence across multiple tested genotyping platforms and a range of samples.

Reference: Burridge, A.J., Wilkinson, P.A., Winfield, M.O., Barker, G.L.A., Allen, A.M., Coghill, J.A., Waterfall, C., and Edwards, K.J. (2018). Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum). Plant Biotechnology Journal 16: 867-876.

Design ID: D10362Ta15K

PaleoChip Arctic-1.0 Plant - Chloroplast barcoding loci panel (trnL, rbcL, matK) for eDNA

NGS enrichment panel designed for capturing plant chloroplast DNA from environmental ancient DNA (‘sedaDNA’) samples. >2K high-latitude plant taxa were covered by the bait design, targeting the trnL, matK, and rbcL loci that are commonly used in eDNA barcoding research. Murchie et al (2020) designed the panel and demonstrated its effectiveness on sedaDNA samples, pooled in a 3:5 ratio (Plant:Animal; total baits/rxn = 200ng) with the separate “Animal” 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: D10184ePLNT

Annonaceae phylogenetics panel

NGS target capture panel targeting 469 exons from the pantropical flowering plant family Annonaceae, with baits designed from transcriptomes of 5 species. Couveur et al (2019) designed the panel and demonstrated its effectiveness for phylogenetic reconstruction broadly across the whole Annonaceae clade (with samples representing all subfamilies), plus demonstrate a species-level relationship reconstruction for a specific tribe (Piptostigmateae; with samples representing all genera).

Reference: Couvreur, T.L.P, A.J. Helmstetter, E.J.M. Koenen, K. Bethune, R.D. Brandão, S.A. Little, H. Sauquet, R.H.J. Erkens. (2018). Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes. Frontiers in Plant Sciences, 9:1941.

Design ID: D10208ANNON

Orchidaceae963 phylogenetics panel

NGS target enrichment panel targeting 963 single-copy genes in the Orchidaeceae flowering plant family, with baits designed from the Phalaenopsis equestris genome. Eserman et al. (2021) designed the panel and demonstrated its effectiveness for phylogenetic research by testing 28 species representing 3 orchid subfamilies. This panel has significant target locus overlap with the Angiosperms353 panel which is also available from Daicel Arbor Biosciences as a myBaits Expert catalog kit.

Reference: Eserman, L.A., S.K. Thomas, E.E.D. Coffey, J.H. Leebens-Mack. (2021). Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci. Applications in Plant Sciences 9(7): e11416.

Design ID: D10052OR963

Senecioneae (of Asteraceae) phylogenetics panel

Enricment panel targeting >1,100 single/low-copy genes in Senecioneae tribe of Asteraceae (sunflower family of flowering plants). Ren et al (2021) designed this panel and demonstrated its effectiveness for phylogenetic research across a set of samples representative of the taxonomic diversity of this group.

Reference: Ren, C., L. Wang, Z-L. Nie, G. Johnson, Q-E. Yang, J. Wen. (2021). Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Molecular Phylogenetics and Evolution 162: 107202.

Design ID: D10338RCPLT

Fungi

Fungal functional gene panel for community profiling in environmental DNA

Enrichment panel targeting fungal genes encoding hydrolytic and oxidative extracellular enzymes and putative general stress tolerance proteins. Moore et al. (2021) designed the panel and demonstrated its effectiveness for studying fungal DNA from environmental soil samples to investigate community profiles of fungal functional genes under different levels of ambient and simulated nitrogen (N) deposition.

Reference: Moore, J.A.M., M.A. Anthony, G.J. Pec, L.K. Trocha, A. Trzebny, K.M. Geyer, L.T.A. van Diepen, S.D. Frey. (2021). Fungal community structure and function shifts with atmospheric nitrogen deposition. Global Change Biology 27:1349–1364.

Design ID: D10341CAZy

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. For example, learn more about our predesigned targeted sequencing service options for wheat.

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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