On-Demand Webinars
Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential
TERESA O’MEARA PHD LAB, UNIVERSITY OF MICHIGAN, DEPARTMENT OF MICROBIOLOGY & IMMUNOLOGY
IDENTIFYING GENOME-WIDE STRUCTURAL VARIATION WITH UST TELL-SEQ™
Candida albicans is a frequent colonizer of human mucosal surfaces and an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is still being determined how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined commensal isolates from healthy donors to identify site-specific phenotypic adaptation and genetic variation associated with these phenotypes. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains and that this genetic diversity includes SNVs and structural rearrangements. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. However, our commensal strains retained the capacity to cause disease in systemic infection models, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans. It suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.
Wet Lab Best Practices: Preserving High-Molecular Weight DNA and Molecular Information 200 Kb or more
Gaining insight into genetic information at the molecular level up to 200 Kb or more is made possible with UST TELL-Seq's™ proven library preparation technology which has been providing this capability to researchers looking for ultra-long-range results for years.
However, when it comes to getting this information from your sequencer, care must be taken during the preparation and handling of DNA when making libraries with UST TELL-Seq™. With years of experience working to preserve this molecular information, the team at Universal Sequencing has identified several areas of the process where extra care should be taken, and solutions to challenges users sometimes face.
Library Preparation and Genome Assembly Using Transposase Enzyme-Linked Long-Read Sequencing (UST TELL-Seq)
In this webinar, Alvaro Hernandez, Ph.D., director of DNA Services at the University of Illinois at Urbana Champaign, will discuss how his team sequenced and assembled the genomes of nine insects using Transposase Enzyme-Linked Long-Read Sequencing (TELL-Seq) at different stages of genome assembly. The unique contributions of TELL-Seq libraries to the completeness of the assembly, as well as the DNA extraction, library preparation, and sequencing methods the team employed, will be discussed in detail.
The insect genomes were sequenced as a pilot project from the University of Illinois Prairie Research Institute, Carl R. Woese Institute for Genome Biology, and the Roy J. Carver Biotechnology Center to demonstrate the potential for Illinois to join a global network of communities engaged in genome assembly and the conservation of biodiversity.
Illumina recently entered into a partnership with Universal Sequencing Technologies, the inventor and distributor of TELL-Seq products, and is sponsoring this webinar to raise awareness of the applications of this novel sequencing technology.
Haplotype Phasing of PCR Amplicons using UST TELL-Seq
Haplotype phasing of genomes and de novo assembly of novel genomes are major hurdles for short read based next generation sequencing platforms. Long sequence reads are essential to overcome the significant sequence homology on some regions of the genome. Several NGS library technology breakthroughs recently have demonstrated barcode linked-read sequencing method can effectively generate long read like information and successfully applied for human genome phasing, structural variation detection or de novo assembly of other genomes. However, they either require expensive capital expenditure on a special instrument or are not scalable for commercial adoption yet due to sophisticated barcode generation. We have developed a simple and scalable NGS library technology, Transposase Enzyme Linked Long-read Sequencing (TELL-SeqTM), to use short NGS reads for genome scale haplotype phasing and/or de novo genome assembly. Several million uniquely barcoded beads are used to generate linked reads, which could be linked as long as a hundred kilobases, by strand transfer reactions using transposase in a PCR tube with a standard NGS laboratory setting. TELL-Seq library procedure takes approximately 3 hours and multiple samples can be easily processed parallelly in a 96-well format when needed. The library protocol can be adjusted and used for various sizes of genomes from bacteria to human. Using TELL-Seq we are able to generate comparable and excellent haplotype phasing results on a NA12878 human sample, and successfully de novo assembly on an E. coli and an Arabidopsis thaliana. More applications and analysis solutions are being developed for TELL-Seq library technology.
Visualization of UST Tell-Sort Data Using the Integrative Genome Viewer
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today’s sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.