Advances in optical mapping for genomic research

Yuxuan Yuan; Claire Yik-Lok Chung; Ting-Fung Chan

doi:10.1016/j.csbj.2020.07.018

Advances in optical mapping for genomic research

Comput Struct Biotechnol J. 2020 Aug 1:18:2051-2062. doi: 10.1016/j.csbj.2020.07.018. eCollection 2020.

Authors

Yuxuan Yuan^{1

2

3}, Claire Yik-Lok Chung^{1

2}, Ting-Fung Chan^{1

2

3}

Affiliations

¹ School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
² State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
³ AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China.

Abstract

Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.

Keywords: 3D, three-dimensional; DBG, de Bruijn graph; DLS, direct label and strain; DNA, deoxyribonucleic acid; Genome assembly; Hi-C, high-throughput chromosome conformation capture; Mb, million base pair; Next generation sequencing; OLC, overlap-layout-consensus; Optical mapping; PCR, polymerase chain reaction; PacBio, Pacific Biosciences; SRS, short-read sequencing; SV, structural variation; Structural variation; bp, base pair; kb, kilobase pair.

Publication types

Review