Chicago® and Dovetail™ Hi-C yield chromosome length scaffolds of the Ixodes scapularis genome
Presented by Monika Gulia-Nuss, University of Nevada, Reno
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 situchromatin 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