Advances in optical mapping for genomic research

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.

Fig 1

Optical mapping milestone timeline. Major breakthroughs in optical mapping over the past two decades are displayed.

Fig 2

Workflow used in optical map production and analysis. Generally, the workflow can be divided into three parts: wet laboratory preparation, optical map generation, and bioinformatics analysis and validation. The essential steps are listed in this figure to show how optical mapping works.

Fig 3

Optical-mapping data analysis. The major bioinformatics analysis steps are illustrated from in silico genome digestion, data quality control, de novo map assembly, map alignment, scaffolding, and SV detection.