Poster Presentation 45th Lorne Genome Conference 2024

Omni-C Enhances Chromosome-Level Accuracy and Refines Abalone Genome Assembly (#102)

Dhanya Sooraj 1 , Roy Barkan 2 3 , Ira Cooke 3 , Jan Strugnell 2 , Sue-Ann Watson 4 5 , Naga Kasinadhuni 6 , Cath Moore 1
  1. Innovation and Development, Australian Genome Research Facility, Melbourne, Victoria, Australia
  2. Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, Queensland , Australia
  3. Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
  4. Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
  5. Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland, Australia
  6. Bioinformatics, Australian Genome Research Facility, Melbourne, Victoria, Australia

The discovery of high throughput chromatin capture (Hi-C) methods1 have significantly accelerated the study of chromatin topology and 3D genomic interactions. Hi-C technology utilizes proximity ligation to provide long- range information that enhances the quality of the genome assembly by guiding the scaffolding of contigs at a chromosomal scale. Dovetail Genomics Omni-C is a sequence-independent endonuclease-based proximity ligation which addresses the limitations of restriction enzyme (RE) based Hi-C approaches to generate proximity ligated DNA fragments that include regions in close spatial proximity but are distant based on their genomic coordinates. Omni-C also supports applications that rely on coverage uniformity - single nucleotide polymorphism (SNP) calling, chromosome phasing, and structural variant detection. The Omni-C is compatible with a wide variety of organisms including mammals, plants, insects and marine invertebrates. 

We have successfully evaluated the Omni-C technology in a range of samples including mammals, insects, and marine invertebrates and here we illustrate how Omni-C scaffolding improved de novo chromosome level assembly of an abalone genome. The built in QC step of Chromatin Digestion Index (CDI) quantitatively predicts the library complexity (in unique molecules per 300 million read pair) and the expected proportion of long-range cis reads are >80%. The QC metrics analysis of Abalone Omni-C library at low pass sequencing shows that valid read pairs- a total of cis>=1kb and trans reads are >85% validates CDI estimation. The QC analysis at 2million (M) read depth also show that the abalone Omni-C generated > 56% mapped reads (MAPQ value >40), ~11% unmapped reads and the complexity (a measure of sufficient diversity) of 105M. Finally, Omni-C significantly improved the chromosome level assembly by generating the largest scaffolds equivalent to 16 chromosome that makes upto 98% of the total abalone genome.

  1. Kaplan, N. , & Dekker, J. (2013). High‐throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology, 31(12), 1143–1147.