Events Archives

Evolution Conference – in person conference June 24-28, 2022

Booths are centrally located in Exhibit Hall C.

myBaits^® Featured Publications
Please browse some recent publications utilizing targeted sequencing with myBaits^® kits and/or myReads^® services for evolutionary biology and ecology research in plants, animals, and more.

Bataillon, T., Gauthier, P., Villesen, P., Santoni, S., Thompson, J. D., & Ehlers, B. K. (2022). From genotype to phenotype: Genetic redundancy and the maintenance of an adaptive polymorphism in the context of high gene flow. Evolution Letters, evl3.277.

Derkarabetian, S., Starrett, J., & Hedin, M. (2022). Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Frontiers in Zoology, 19(1), 8.

Hart, P. B., Arnold, R. J., Alda, F., Kenaley, C. P., Pietsch, T. W., Hutchinson, D., & Chakrabarty, P. (2022). Evolutionary Relationships Of Anglerfishes (Lophiiformes) Reconstructed Using Ultraconserved Elements. Molecular Phylogenetics and Evolution, 107459.

Kearns, A. M., Campana, M. G., Slikas, B., Berry, L., Saitoh, T., Cibois, A., & Fleischer, R. C. (2022). Conservation genomics and systematics of a near-extinct island radiation. Molecular Ecology, 31(7), 1995-2012.

Manuzzi, A., Jiménez-Mena, B., Henriques, R., Holmes, B. J., Pepperell, J., Edson, J., Bennett, M. B., Huveneers, C., Ovenden, J. R., & Nielsen, E. E. (2022). Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population. Scientific Reports, 12(1), 6582.

Montes, J., Peláez, P., Moreno‐Letelier, A., & Gernandt, D. S. (2022). Coalescent‐based species delimitation in North American pinyon pines using low‐copy nuclear genes and plastomes. American Journal of Botany, ajb2.1847.

Parker, L. D., Campana, M. G., Quinta, J. D., Cypher, B., Rivera, I., Fleischer, R. C., Ralls, K., Wilbert, T. R., Boarman, R., Boarman, W. I., & Maldonado, J. E. (2022). An efficient method for simultaneous species, individual, and sex identification via in‐solution single nucleotide polymorphism capture from low‐quality scat samples. Molecular Ecology Resources, 22(4), 1345–1361.

Patrono, L. V., Röthemeier, C., Kouadio, L., Couacy‐Hymann, E., Wittig, R. M., Calvignac‐Spencer, S., & Leendertz, F. H. (2022). Noninvasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture. Influenza and Other Respiratory Viruses, irv.12984.

Singhal, S., Colli, G. R., Grundler, M. R., Costa, G. C., Prates, I., & Rabosky, D. L. (2022). No link between population isolation and speciation rate in squamate reptiles. Proceedings of the National Academy of Sciences, 119(4).

Stiller, J., Short, G., Hamilton, H., Saarman, N., Longo, S., Wainwright, P., Rouse, G. W., & Simison, W. B. (2022). Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biology, 20(1), 75.

Stoek, F., Barry, Y., Ba, A., Schulz, A., Rissmann, M., Wylezich, C., Sadeghi, B., Beyit, A. D., Eisenbarth, A., N’diaye, F. B., Haki, M. L., Doumbia, B. A., Gueya, M. B., Bah, M. Y., Eiden, M., & Groschup, M. H. (2022). Mosquito survey in Mauritania: Detection of Rift Valley fever virus and dengue virus and the determination of feeding patterns. PLOS Neglected Tropical Diseases, 16(4), e0010203.

Weise, E. M., Scribner, K. T., Adams, J. V., Boeberitz, O., Jubar, A. K., Bravener, G., Johnson, N. S., & Robinson, J. D. (2022). Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology Evolutionary Applications, eva.13364.

The Essential Protein Engineering & Cell Therapy Summit

PEGSummit.com

PAG 2022 Website

Daicel Arbor Biosciences – Booth #310

We are sorry that PAG was canceled. Our scientists really want to meet you virtually to learn about your scientific achievements and to discuss your new projects. You can use the ZOOM Meeting link here from 9:00 a.m. to 5:00 p.m., EST, on January 10, to talk to our scientists. Please click here for link.

Welcome to the PAG 2022 web page for Daicel Arbor Biosciences. Thank you for visiting. Please click on one of the sections below for additional information.

Our Industry Workshops

Location: Palm 1-2

Date: Monday, January 10, 12:50 p.m.

Speakers:

Jacob Enk, PhD (Daicel Arbor Biosciences) – 12:55 p.m. PT – Introduction to Renseq from Daicel Arbor Biosciences
Sanu Arora, PhD (John Innes Centre) – 1:15 p.m. PT – Understanding the Genetic Basis of Disease Resistance in Peas
Ingo Hein, PhD (James Hutton Institute) – 1:35 p.m. PT
Tim Hewitt, PhD (CSIRO) – 1:55 p.m. PT – Target Acquired: Using Renseq on Knockout Mutants to Rapidly Clone R Genes in Wheat

The resistance gene enrichment sequencing (RenSeq) workflow supports the comprehensive study of highly complex disease resistance gene (R-gene) families within crop plant genomes. Over the last few years, RenSeq and related NGS approaches have been utilized in or contributed to hundreds of studies across a wide range of plant species. In this workshop, we will highlight the major principles, benefits, and recent advances of RenSeq, and hear from several leading researchers who are actively utilizing it and related NGS techniques in their crop research programs, facilitated by myBaits® Custom hybridization capture kits.

More Info

Poster Presentations from Daicel Arbor Biosciences & Collaborators

Number PE0340

Authors: Junli Zhang, German Burguener, Juan Debernardi, Frederic Choulet, Etienne Paux, Jacob Enk, Jorge Dubcovsky

As genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here we present a regulatory region NGS hybridization capture panel developed for hexaploid and tetraploid wheat. We used the upstream ~2 kbp of each annotated gene in the most up-to-date Chinese Spring wheat genome assembly as the primary target source, supplemented with homologous sequences from a draft assembly of tetraploid Kronos wheat as well as regions of observed open chromatin state identified with ATACseq. To improve specificity compared to similar legacy designs, candidate repetitive sequences were aggressively filtered using a combination of cross-alignment clustering, TREP19 affinity filtration, and kmer frequency capping. Once converted to candidate probes, these were once again filtered for specificity using a standard design pipeline, resulting in a final target space of ~175 Mbp relative to the IWGSC RefSeq v1.0 genome. Test captures using the probe set on both hexaploid and tetraploid wheat exhibit excellent coverage of the target with significantly improved specificity compared to captures performed using legacy probe designs. Captures of 24 lines from the Kronos TILLING population (EMS-induced mutations) detected an average of ~3300 mutations per line (~5 million predicted mutations in the complete TILLING population of 1500 lines). This probe set is available through Daicel Arbor Biosciences as either a stand-alone capture kit or a full service option from library prep through secondary bioinformatics analysis.

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Genomic Regulatory Element Sequencing in Wheat

Number PO0409

Authors: Brian Brunelle, Alison Devault, Jacob Enk and Tina Lan, Daicel Arbor Biosciences, Ann Arbor, MI

The detection of pathogenic variants and pathobiome profiling in plant and animal samples using next-generation sequencing (NGS) is often impeded by the dominant host/background DNA and/or RNA, necessitating extremely deep total NGS in order to accurately resolve genomes/genes of interest or to fully characterize community members. Targeted NGS methods can dramatically reduce the overall costs of sequencing and data analysis per sample. Of the available targeted NGS methods, hybridization capture is the best technique for comprehensive, low-bias, and cost-effective genome or community sequencing of viruses and bacteria from complex samples. Here we review the principles of hybridization capture for microbial sequencing applications, and highlight several peer-reviewed studies relevant to the plant and animal research community, powered by efficient myBaits® target capture kits.

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Simplified Pathogen and Commensal Sequencing

Product Sheets and Application Notes

Click on the product below to view PDF.

myTags

[ab_icon icon=”file-pdf-o”] myTags Chromosome Indexing by FISH App Note

[ab_icon icon=”file-pdf-o”] myTags Custom Product Sheet

myReads

[ab_icon icon=”file-pdf-o”] myReads NGS Services Product Sheet

myBaits

[ab_icon icon=”file-pdf-o”] myBaits Hybridization Capture Kits Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom DNA Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom RNA Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom Methyl Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Microbial Targeted Genomics App Note

[ab_icon icon=”file-pdf-o”] myBaits NLR_Gene_Resequencing Expression using cDNA RenSeq App Note

myTXTL

[ab_icon icon=”file-pdf-o”] myTXTL Product Sheet

myCurio

[ab_icon icon=”file-pdf-o”] Curio

Claim your special PAG gift!

Since we cannot personally hand you our great booth gift, you can claim it using promotion code DAB PAG 2022 at Daicel Arbor PAG gift.

myTags Custom FISH Probes

myReads NGS Services

myBaits Expert Wheat Exome Panel

myBaits Custom Panels

ASHG 2020 is the largest human genetics meeting and exposition in the world. This year’s virtual meeting is expected to attract over 4,000 scientific attendees, plus 70 exhibiting companies, powering all areas of innovation the field from microscopes to data storage and analytics. The meeting provides a forum for the presentation and discussion of cutting-edge science in all areas of human genetics. Stop by Daicel Arbor Biosciences booth and connect with us!

CSHL – Genome Organization & Nuclear Function

Cold Spring Harbor, NY

This will now be a virtual meeting to accommodate attendees across the globe during the current COVID-19 outbreak.

DOE JGI User Meeting

Postponed until Fall 2020

Oakland, CA

PAG XXVIII Website

Booth #308

San Diego, CA

Summary of Industry Workshops

Advances in Visualizing Genome Organization – from Haplotypes to Chromosomal Barcoding

James A. Birchler – University of Missouri
Whole chromosome paints have previously been developed for each chromosome of maize that rely on thousands of unique oligonucleotide probes along the length of each chromosome. This set is genotype independent and will label the respective chromosome across all tested maize lines. With the availability of genomic sequences for both B73 and Mo17 inbred lines, the ability to generate probe collections specific to those genotypes is available. Toward this end, Presence/Absence Variation (PAV) and SNPs were used for predicted oligos from one inbred sequence that were absent in the other and vice versa for chromosome 10 from the respective inbreds. The developed oligopaints were effective at distinguishing the two homologues of 10 in a B73/Mo17 hybrid. These haplotype specific probe sets were used to visualize recombination events from progeny of a B73/Mo17 hybrid and in Recombinant Inbred Line populations that fix recombination events from the two parental lines. Ongoing studies are examining the behavior of homologues in meiosis.

Kai Wang – Fujian Agriculture and Forestry University

Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world’s sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, oligo-FISH technology was optimized and a suitable system for sugarcane was established. The creation of oligo-FISH remarkably improves our ability to conduct cytological research on sugarcane, and bring us deep insights into the genomic structure and evolution of sugarcane.

Takayoshi Ishii – Arid Land Research Center, Tottori university

Andreas Houben – Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

We developed a tool to visualize defined genomic sequences in fixed nuclei and chromosomes based on a two-part guide RNA with the recombinant Cas9 endonucleasecomplex. In contrast to classical in situhybridization, RGEN-ISL (RNA-guided endonuclease – in situ labelling) does not require DNA denaturation and therefore permits a better structural chromatin preservation. The application of differentially labelled tracrRNAs allows the multiplexing of RGEN-ISL. We established a combination of RGEN-ISL, immuno-staining and EdU labelling to visualize in situ specific repeats, histone marks and DNA replication sites, respectively. The broad range of adaptability of RGEN-ISL to different temperatures and combinations of methods has the potential to advance the ﬁeld of chromosome biology.

Complete Wheat Exome Analysis – From DNA to Variant Calling

Burkhard Steuernagel – The Sainsbury Laboratory and John Innes Centre

Disease resistance in plants is often conferred by members of a gene family that encode for intracellular receptors. These receptors have a nucleotide binding domain and leucine rich repeats (NLR). Resistance-gene Enrichment Sequencing (RenSeq) targets NLR genes and enables several cost-effective methods to identify such genes. We have designed RenSeq bait libraries for wheat and used them in combination with two complementary approaches. MutRenSeq deploys mutational genomics to target specific resistance genes. AgRenSeq is used for association genetics in a natural diversity panel. Both techniques have been used to identify several novel genes.

Shawn Quinn – Curio Genomics

As part of a collaboration with Daicel Arbor Biosciences the extensible Curio Genomics platform serves as the foundation that enables interpretive and real time analysis of NGS data generated from libraries that are enriched to focus on the high-confidence exon-annotated genome in hexaploid wheat.

In this talk we will demonstrate specific examples of how the platform scales to allow research partners to efficiently ask compound and complex bioinformatic questions of the massive genome of Chinese Spring Wheat samples. We’ll also show how the platform’s unique approach to the storage and processing of wheat genome data empowers researchers to conveniently collaborate with others, perform analyses, compare between samples, change analytical settings, apply different filters, and visualize results – all in real time.

Ute Baumann – The University of Adelaide

Posters Presentations from Daicel Arbor Biosciences & Collaborators

Multi-Cultivar Wheat Tetraploid and Hexaploid Exome Capture with a Single Enrichment Kit

Cannabis sativa Genotyping and Exon Sequencing Using a New Jamaican Lion-Derived Hybridization Capture Panel

SMRT-RenSeq for NLR Resistance Gene Characterization in Arachis, Glycine and Musa Species

Meiotic Crossovers Characterized by Haplotype- Specific Chromosome Painting in Maize

myTags® Synthetic FISH Probes Design Schemes for Plant and Animal Molecular Cytogenetics – Recombination, Translocation, Ploidy and Karyotyping Applications

Palaeochip: A Capture Enrichment Approach to Ancient Environmental DNA