More requirements for whole genome sequencing analysis: size and chromatin conformation of nuclear DNA

Abstract

Advancing DNA sequencing technologies have enabled the acquisition of whole genome sequences of diverse species including targets of aquaculture and conservation, which assists more evidence-based understanding of population as well as the molecular basis of biological phenomena charactering individual species. After the complete sequencing of the human genome was finally achieved, the ‘telomere-to-telomere (T2T)’ grade of whole genome assembly, namely devoid of any undetermined regions, is around the corner for other species. Although DNA sequencing per se is fulfilled with the use of extracted DNA molecules literally, the completion of whole genome assembly requires higher-order evidence of intra-chromosomal linkages of DNA sequences that can be captured from chromatin conformation in the nucleus. Moreover, its product should be validated with the expected size of the genome that is measured independently of DNA sequencing. This article outlines the non-trivial nature of these ‘non-sequencing’ techniques and their importance in modern whole genome assembly and summarizes the authors’ original effort to optimize the use of the techniques.