A Universal Phylogenomics Solution for Flowering Plants

The myBaits Expert Angiosperms353 kit has been demonstrated to work across a very wide taxonomic and sample range, with excellent exonic and intronic recovery that varies depending on the species and the quality of DNA input. Some example data are shown below, but for the latest and most comprehensive results, check out the most recent Publications that have been published utilizing this kit for an even greater variety of species and sample types.

Fig 1. “Heatmap of Gene Recovery Efficiency. Each row is one sample, and each column is one gene. Colors indicate the percentage of the target length (calculated by the mean length of all k-medoid transcripts for each gene) recovered.” (pg 19, Johnson, Pokorny, Dodsworth et al 2019, Syst Bio). Image is Figure 3 from Johnson, Pokorny, Dodsworth et al 2019, Syst Biol.

Fig 2. “Total Length of Sequence Recovery for Both Coding and Non-coding Regions Across 353 Loci for 42 Angiosperm Species. Reads were mapped back to either coding sequence (yellow) or coding sequence plus flanking non-coding (i.e. intron) sequence (purple)… The total length of coding sequence targeted was 260,802 bp. The median recovery of coding sequence was 137,046 bp and the median amount of non-coding sequence recovered was 216,816 bp (with at least 8x depth of coverage).” (pg 21, Johnson, Pokorny, Dodsworth et al 2019, Syst Bio). Image is modified version of Figure 4 from Johnson, Pokorny, Dodsworth et al 2019, Syst Bio.

Angiosperms353 Resources

Original Publication
Johnson, M., Pokorny, L., Dodsworth, S., Botigue, L.R., Cowan, R.S., Devault, A., … Wickett, N. (2019). A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. Systematic Biology 68(4): 594-606
GitHub Repository: HybSeq Target Capture of 353 Protein Coding Genes in Any Angiosperm

Related Tools and Reviews
See “Publications” tab for additional papers that utilize the Angiosperms-353 kit.

• Dodsworth, S., Pokorny, L., Johnson, M.G., Kim, J.T., Maurin, O., Wickett, N.J., … Baker, W.J. (2019). Hyb-Seq for Flowering Plant Systematics. Trends in Plant Science 24, 887–891.
• Hale, H., Gardner, E.M., Viruel, J., Pokorny, L., Johnson, M.G., (2020). Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Applications in Plant Sciences 8, e11337.
• Slimp, M., Williams, L. D., Hale, H., Johnson, M.G. (2021). On the potential of Angiosperms353 for population genomic studies. Applications in Plant Sciences 9( 7): e11419.
• McLay, T.G., Birch, J.L., Gunn, B.F., Ning, W., Tate, J.A., Nauheimer, L., … Forest, F. (2021). New targets acquired: improving locus recovery from the Angiosperms353 probe set. Applications in Plant Sciences.
• Nauheimer, L., Weigner, N., Joyce, E., Crayn, D., Clarke, C., Nargar, K. (2021). HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets. Applications in Plant Sciences.
• McDonnell, A.J., Baker, W.J., Dodsworth, S., Forest, F., Graham, S. W., … Wickett, N.J. (2021). Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. Applications in Plant Sciences 9(7): e11443.
• Baker, W.J., Dodsworth, S., Forest, F., Graham, S.W., Johnson, M. G., McDonnell, A., … Wickett, N.J. (2021). Exploring Angiosperms353: an open, community toolkit for collaborative phylogenomic research on flowering plants. American Journal of Botany 108(7): 1059–1065.

Poster – PAGXXVII – “A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant”

Kew Tree of Life Explorer: “Building a comprehensive evolutionary tree of life for flowering plants”

PAFTOL (Plant and Fungal Trees of Life) Project: “Discovering and disseminating the evolutionary history of all plant and fungal genera”

myBaits Kit Protocol

Current Version: v5

myBaits Manual v5
For kits shipped starting in Sept 2020, with Cat#’s ending in “.v5”

Safety Data Sheet

myBaits Kit SDS – US Version – v5 Chemistry – Sept 2020

myBaits Kit SDS – EU Version – v5 Chemistry – Sept 2020

Visit the SDS resources page to download previous versions.

Featured Publications

The publications listed below highlight some uses of the myBaits^® Expert Angiosperms353 hyb capture kit in various plant genetics applications. A more comprehensive searchable database of hundreds of myBaits publications is available on our general Daicel Arbor Biosciences publications page. Thank you to all our new and returning clients for trusting myBaits for your innovative research projects!

• Antonelli, A., Clarkson, J.J., Kainulainen, K., Maurin, O., Brewer, G.E., Davis, A.P., … Baker, W.J. (2021). Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. American Journal of Botany 108, 1143–1165.
• Baker, W.J., Bailey, P., Barber, V., Barker, A., Bellot, S., Bishop, D., … Forest, F. (2021). A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Systematic Biology.
• Brewer, G.E., Clarkson, J.J., Maurin, O., Zuntini, A.R., Barber, V., Bellot, S., … Baker, W.J. (2019). Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms. Front. Plant Sci. 0.
• Buerki, S., Callmander, M.W., Acevedo-Rodriguez, P., Lowry, P.P., Munzinger, J., Bailey, P., … Forest, F. (2021). An updated infra-familial classification of Sapindaceae based on targeted enrichment data. American Journal of Botany 108, 1234–1251.
• Clarkson, J.J., Zuntini, A.R., Maurin, O., Downie, S.R., Plunkett, G.M., Nicolas, A.N., … Baker, W.J., (2021). A higher-level nuclear phylogenomic study of the carrot family (Apiaceae). American Journal of Botany 108, 1252–1269.
• Gaynor, M.L., Fu, C.-N., Gao, L.-M., Lu, L.-M., Soltis, D.E., Soltis, P.S. (2020). Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis. Journal of Systematics and Evolution 58, 646–662.
• Hendriks, K.P., Mandáková, T., Hay, N.M., Ly, E., Huysduynen, A.H. van, Tamrakar, R., … Bailey, C.D. (2021). The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. Applications in Plant Sciences 9.
• Johnson, M., Pokorny, L., Dodsworth, S., Botigue, L.R., Cowan, R.S., Devault, A., … Wickett, N. (2019). A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. Systematic Biology 68(4): 594-606.
• Larridon, I., Villaverde, T., Zuntini, A.R., Pokorny, L., Brewer, G.E., Epitawalage, N., … Baker, W.J. (2020). Tackling Rapid Radiations With Targeted Sequencing. Frontiers in Plant Science 10: 1.
• Larridon, I., Zuntini, A.R., Barrett, R.L., Wilson, K.L., Bruhl, J.J., Goetghebeur, P., … Roalson, E.H. (2021). Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing. Botanical Journal of the Linnean Society 196, 163–187.
• Larridon, I., Zuntini, A.R., Léveillé-Bourret, É., Barrett, R.L., Starr, J.R., Muasya, A.M., … Baker, W.J. (2021). A new classification of Cyperaceae (Poales) supported by phylogenomic data. Journal of Systematics and Evolution 59, 852–895.
• Lee, A.K., Gilman, I.S., Srivastav, M., Lerner, A.D., Donoghue, M.J., Clement, W.L. (2021). Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights. American Journal of Botany 108, 1122–1142.
• Maurin, O., Anest, A., Bellot, S., Biffin, E., Brewer, G., Charles-Dominique, T., … Lucas, E. (2021). A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. American Journal of Botany 108(7): 1087–1111.
• Murphy, B., Forest, F., Barraclough, T., Rosindell, J., Bellot, S., Cowan, R., … Cheek, M. (2020). A phylogenomic analysis of Nepenthes (Nepenthaceae). Molecular Phylogenetics and Evolution 144, 106668.
• Ogutcen, E., Christe, C., Nishii, K., Salamin, N., Möller, M., Perret, M. (2021). Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Molecular Phylogenetics and Evolution 157, 107068.
• Ottenlips, M.V., Mansfield, D.H., Buerki, S., Feist, M.A.E., Downie, S.R., Dodsworth, … Smith, J.F. (2021). Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex. American Journal of Botany 108, 1217–1233.
• Pérez-Escobar, O.A., Dodsworth, S., Bogarín, D., Bellot, S., Balbuena, J.A., Schley, R.J., … Baker, W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany 108, 1166–1180.
• Pillon, Y., Hopkins, H.C.F., Maurin, O., Epitawalage, N., Bradford, J., Rogers, Z.S., … Forest, F. (2021). Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments. American Journal of Botany 108, 1181–1200.
• Shah, T., Schneider, J.V., Zizka, G., Maurin, O., Baker, W., Forest, F., … Larridon, I., (2021). Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. American Journal of Botany 108, 1201–1216.
• Shee, Z. Q., D. G. Frodin, R. Cámara-Leret, L. Pokorny. (2020). Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. Frontiers in Plant Science 11: 258.
• Siniscalchi, C.M., Hidalgo, O., Palazzesi, L., Pellicer, J., Pokorny, L., Maurin, O., … Mandel, J.R. (2021). Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. Applications in Plant Sciences 9.
• Starr, J.R., Jiménez-Mejías, P., Zuntini, A.R., Léveillé-Bourret, É., Semmouri, I., Muasya, M., … Larridon, I. (2021). Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l. Journal of Systematics and Evolution 59, 809–832.
• Thomas, A.E., Igea, J., Meudt, H.M., Albach, D.C., Lee, W.G., Tanentzap, A.J. (2021). Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. American Journal of Botany 108, 1289–1306.
• Thomas, S.K., Liu, X., Du, Z.-Y., Dong, Y., Cummings, A., Pokorny, L., … Leebens-Mack, J.H. (2021). Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set. American Journal of Botany 108, 1112–1121.
• Ufimov, R., Zeisek, V., Píšová, S., Baker, W.J., Fér, T., Loo, M., … Schmickl, R. (2021). Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae. Applications in Plant Sciences 9, e11442.
• Van Andel, T., Veltman, M. A., Bertin, A., Maat, H., Polime, T., Hille Ris Lambers, D., … Manzanilla, V.. (2019). Hidden Rice Diversity in the Guianas. Frontiers in Plant Science 10: 1161.
• Wenzell, K.E., McDonnell, A.J., Wickett, N.J., Fant, J.B., Skogen, K.A. (2021). Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja. American Journal of Botany 108, 1270–1288.
• Zuntini, A.R., Frankel, L.P., Pokorny, L., Forest, F., Baker, W.J. (2021). A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. American Journal of Botany 108, 1066–1086.

For links to hundreds more myBaits publications, visit the publications page!