OCT 23, 2018 9:00 AM PDT

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

Sponsored by: Dovetail Genomics
Speaker
  • 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™)

     


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