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      Advances in optical mapping for genomic research

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          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.

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          Opportunities and challenges in long-read sequencing data analysis

          Shanika Amarasinghe, Shian Su, Xueyi Dong … (2020)
          Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long-read data are thus required, but the fast pace of development of such tools can be overwhelming. To assist in the design and analysis of long-read sequencing projects, we review the current landscape of available tools and present an online interactive database, long-read-tools.org, to facilitate their browsing. We further focus on the principles of error correction, base modification detection, and long-read transcriptomics analysis and highlight the challenges that remain.
          Article 0 comments Cited 510 times – based on 0 reviews     Review now
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            Mapping and sequencing of structural variation from eight human genomes.

            Jeffrey M. Kidd, Gregory M. Cooper, William F Donahue … (2008)
            Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.
            Article 0 comments Cited 366 times – based on 0 reviews     Review now
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              Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

              Jia-Ming Song, Zhilin Guan, Jianlin Hu … (2020)
              Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.
              Article 0 comments Cited 244 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Ting-Fung Chan
                Journal
                Journal ID (nlm-ta): Comput Struct Biotechnol J
                Journal ID (iso-abbrev): Comput Struct Biotechnol J
                Title: Computational and Structural Biotechnology Journal
                Publisher: Research Network of Computational and Structural Biotechnology
                ISSN (Electronic): 2001-0370
                Publication date PMC-release: 01 August 2020
                Publication date Collection: 2020
                Publication date (Electronic): 01 August 2020
                Volume: 18
                Pages: 2051-2062
                Affiliations
                [a ]School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
                [b ]State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
                [c ]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
                Author notes
                [* ]Corresponding author at: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China. tf.chan@ 123456cuhk.edu.hk
                [1]

                These authors contributed equally.

                Article
                Publisher ID: S2001-0370(20)30350-0
                DOI: 10.1016/j.csbj.2020.07.018
                PMC ID: 7419273
                PubMed ID: 32802277
                SO-VID: c5ca8a49-3555-4b89-8687-1c4250c49e0c
                Copyright © © 2020 The Author(s)
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 10 May 2020
                Date revision received : 8 July 2020
                Date accepted : 24 July 2020
                Categories
                Subject: Review Article

                Keywords: bp, base pair,dbg, de bruijn graph,dls, direct label and strain,dna, deoxyribonucleic acid,hi-c, high-throughput chromosome conformation capture,kb, kilobase pair,mb, million base pair,olc, overlap-layout-consensus,pacbio, pacific biosciences,pcr, polymerase chain reaction,srs, short-read sequencing,sv, structural variation,3d, three-dimensional,optical mapping,genome assembly,structural variation,next generation sequencing
                Data availability:
                Keywords: bp, base pair, dbg, de bruijn graph, dls, direct label and strain, dna, deoxyribonucleic acid, hi-c, high-throughput chromosome conformation capture, kb, kilobase pair, mb, million base pair, olc, overlap-layout-consensus, pacbio, pacific biosciences, pcr, polymerase chain reaction, srs, short-read sequencing, sv, structural variation, 3d, three-dimensional, optical mapping, genome assembly, structural variation, next generation sequencing

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