OCT 23, 2018 09:00 AM PDT

Chicago® and Dovetail™ Hi-C yield chromosome length scaffolds of the Ixodes scapularis genome

SPONSORED BY: Dovetail Genomics
Speakers
  • Assistant Professor in the Department of Biochemistry and Molecular Biology at the University of Nevada, Reno
    Biography
      Monika Gulia-Nuss is an Assistant Professor in the Department of Biochemistry and Molecular Biology at the University of Nevada, Reno. Dr. Gulia-Nuss's research focuses on understanding the basic biology of ticks in order to identify novel targets for tick control. Her long-term goal is to develop novel strategies to control ticks and tick-borne disease transmission. To this end, she is generating first-ever transgenic ticks using CRISPR-Cas gene-editing system and employing other cutting-edge genomic techniques such as Hi-C based genome scaffolding for better assembly and annotation of the tick genome. Her current work focuses on understanding the role of insulin signaling in tick-pathogen interactions and differences in chemoreception circuit in different Ixodes species. Understanding tick- pathogen interactions and genes involved in host seeking are vital to development of novel disease transmission control strategies.

    Abstract:

    DATE: October 23, 2018
    TIME: 9:00AM PDT

    Ixodes scapularis is the principal vector of the Lyme disease spirochete, Borrelia burgdorferi. I. scapularis genome was the first and only medically important acarine species sequenced and annotated thus far. The genome was sequenced using BAC clones and Sanger sequencing methods. However, the 2.1 Gb haploid genome with long repetitive sequencing posed challenge to achieve scaffolds that span entire chromosomes. Some repetitive regions were too large and difficult to be spanned by the available clone libraries. The assembly, IscaW1, comprises 369,495 scaffolds representing 57% of the genome. The fragmented genome further poses challenges in identifying gene sequences and therefore a high-quality genome sequence is needed for advance genomics and genetics work in this vector.

    The availability of sequencing methods that could produce scaffold size sequence length and three-dimensional chromatin capture such as PacBio, and Dovetail Hi-C, respectively, are changing the genome sequencing landscape. Hi-C is a sequencing-based approach for determining how a genome is folded by measuring the frequency of contact between pairs of loci. Dovetail™ Hi-C data can provide links across a variety of length scales, spanning even whole chromosomes and this technique has been used to improve draft genome assemblies and to create chromosome-length scaffolds for large genomes. We therefore used the Dovetail Hi-C technique to achieve chromosomal level assembly of tick genome. We carried out Chicago® and Dovetail Hi-C assemblies that utilize in vitro and in situ chromatin structures, respectively, in order to provide the best scaffolding success. We successfully assembled the genome in 28 >10Mbp sequences that correspond to 28 chromosomes in I. scapularis.

    Learning Objective:

    • The value of obtaining a highly contiguous and accurate genome assembly up to chromosome scale for a highly repetitive genome.

     

    Dovetail Genomics is transforming the life sciences by profiling the 3-dimensional structure of the genome. Dovetail’s proprietary in vitro proximity ligation approach and assembly algorithms enable researchers and clinicians to solve complex problems involving de novo assembly, structural variation, microbiome analysis, TAD analysis, cancer research, phasing analysis and more.

    Contact us: dovetailgenomics.com | 831.713.4465 | info@dovetail-genomics.com

    Learn More: The Dovetail Genome Assembly Award Program (DT-GAAP™)

     


    Show Resources
    You May Also Like
    MAY 03, 2018 11:00 AM PDT
    MAY 03, 2018 11:00 AM PDT
    DATE: May 3, 2018TIME: 11:00AM PDT, 2:00PM EDTWhile stress is one of the leading causes of neuropsychiatric disorders, the molecular underpinnings of how stress induces alterations in b...
    MAY 22, 2018 08:00 AM PDT
    C.E. CREDITS
    MAY 22, 2018 08:00 AM PDT
    DATE: May 22, 2018TIME: 08:00AM PDT The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are closely related transcription factors that...
    APR 27, 2018 10:00 AM PDT
    C.E. CREDITS
    APR 27, 2018 10:00 AM PDT
    DATE: April 27, 2018TIME: 10:00am PST, 1:00pm ESTGlioblastoma (GBM) and Medulloblastoma (MB) are the most common adult and paediatric brain tumours, both of which can have devastating c...
    JUN 29, 2018 09:00 AM PDT
    C.E. CREDITS
    JUN 29, 2018 09:00 AM PDT
    DATE: June 29, 2018TIME: 09:00AM PDT, 12:00PM EDT There is significant epidemiological evidence to suggest that the consumption of a high-broccoli diet is associated with a r...
    MAY 24, 2018 09:30 AM PDT
    C.E. CREDITS
    MAY 24, 2018 09:30 AM PDT
    DATE: May 24, 2018 TIME: 9:30PM PDT The current gold standard in in vitro pre-clinical cancer treatment screening remain cell lines,...
    AUG 15, 2018 08:00 AM PDT
    C.E. CREDITS
    AUG 15, 2018 08:00 AM PDT
    DATE: August 15, 2018TIME: 08:00AM PDT, 11:00AM EDTThe failure of current chemotherapeutic strategies in the fight against cancer can be largely attributed to the occurrence of drug res...
    Loading Comments...