Overview
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 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.
Daicel Arbor is your source for myBaits Custom panels designed by researchers and available to support your plant and fungal genetics research.
Have a suggestion to add a new panel to our list? Contact us today.
Plants
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
Asparagus phylogenetics panel
Asparagaceae1726 is a target enrichment panel targeting 1726 low-copy nuclear genes for Hyb-Seq and phylogenomics in the angiosperm family Asparagaceae. Bentz and Leebens-Mack (2024) validated this panel in 6 of the 7 subfamilies of Asparagaceae, yielding high rates of target capture, and demonstrated its effectiveness for phylogenomics in the family. 206 target loci in this panel overlap with the Angiosperms353 panel, which is also available from Daicel Arbor Biosciences as a myBaits Expert catalog kit. Asparagaceae1726 target and probe sequences can be found on GitHub at https://github.com/bentzpc/Asparagaceae1726.
Reference: Bentz, P.C. and J. Leebens-Mack. (2024). Developing Asparagaceae1726: an Asparagaceae-specific probe set targeting 1,726 loci for Hyb-Seq and phylogenomics in the family. Applications in Plant Sciences.
Design ID: D10063Aspar
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
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
Senecioneae (of Asteraceae) phylogenetics panel
Enrichment 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
Wheat Regulome V1 - Wheat regulatory elements panel
Large next-generation sequencing enrichment panel demonstrated to broadly and efficiently enrich promoter and 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.
Reference: Zhang, J., J.M. Debernardi, G.F. Burguener, F. Choulet, E. Paux, L. O’Connor, J. Enk, J. Dubcovsky. (2022). A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives. The Plant Genome 16(1): e20296
Design ID: D10107WtPrm
Protocol: myBaits Wheat Exome Manual
Wheat Genotyping - 15K
Enrichment panel targeting ~15K genotyping SNP markers in hexaploid wheat (Triticumaestivum). 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
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.
myBaits kits are for research use only and are not validated for diagnostic or therapeutic purposes.
Publications
The featured publications listed below correspond to our collection of Community Panels. Daicel Arbor Biosciences thanks these authors for sharing their probe designs for the benefit of the wider research community. For more published papers that utilize myBaits Custom and Expert kits, please visit our Publications page.
Molecular Phylogenetics and Evolution | September 1, 2021
Global Change Biology | April 1, 2021
Fungal community structure and function shifts with atmospheric nitrogen deposition
Applications in Plant Sciences | January 1, 2021
Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci
Frontiers in Plant Science | January 9, 2019
Plant Biotechnology Journal | January 1, 2017
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.
myBaits kits are for research use only and are not validated for diagnostic or therapeutic purposes.
Resources
myBaits kits are for research use only and are not validated for diagnostic or therapeutic purposes.
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