Chicago and Dovetail Hi-C proximity ligation yield chromosome length scaffolds of Ixodes scapularis genome

Abstract

A high-quality genome sequence is essential for understanding an organism on molecular level. However, the larger genomes with substantial repetitive sequences are challenging to assemble with the sequencing technologies. Hi-C technique is changing the genome architecture landscape by providing links across a variety of length scales, spanning even whole chromosomes. Ixodes scapularis haploid genome is 2.1 gbp and the current assembly consists of 369,495 scaffolds representing 57% of the genome. The fragmented genome poses challenges with functional gene analysis and an improved assembly is needed. We therefore used the Hi C technique to achieve chromosomal level assembly of tick genome. With Chicago and Dovetail Hi C assemblies, we were able to achieve 28 >10Mb sequences that correspond to 28 chromosomes in I. scapularis.

High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense

“…In addition, Dovetail Genomics' HiRise pipeline generated a HiC linkage density histogram plot (Figure 2). The plot compares the positions of read pair sequences (the pair of end sequences from each and every sequenced DNA fragment obtained by chromatin crosslinking) versus the positions of each individual DNA sequence within the genome assembly 10,17 . The alignment produces a diagonal of lines from lower left to upper right in the plot that represent each of the 12 pseudo-chromosomes.…”

Genetic Manipulation of Ticks: A Paradigm Shift in Tick and Tick-Borne Diseases Research

“…The availability of tick genome sequences ( Cramaro et al., 2015 ; Gulia-Nuss et al., 2016 ; Cramaro et al., 2017 ; Nuss et al., 2018 ; Jia et al., 2020 ) have already made application of molecular methods possible in ticks. However, study of the molecular biology of ticks is currently limited by the applicability of genetic tools.…”

Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data

“…One natural question that arises with any new genome assembly is how one assesses that an assembly is “ correct .” Indeed, some of the recently published Hi-C–based assemblies have not provided any corroborating evidence supporting their assemblies (e.g., [ 51 ]). Here, we used 3 independent sources of information to provide evidence that 11 of 12 large syntenic differences identified from the dot plots are correct in our new baboon assembly (Panubis1.0) relative to the previous assembly Panu_3.0 (Table 2 ).…”