Bacteriophage strain typing by rapid single molecule analysis

Grunwald, Assaf; Dahan, Maxime; Giesbertz, Anna; Nilsson, Anne; Nyberg, Lena; Weinhold, Elmar G.; Ambjörnsson, Tobias; Westerlund, Fredrik; Ebenstein, Yuval

doi:10.1093/nar/gkv563

Cited by 66 publications

(97 citation statements)

References 38 publications

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“…Since this type of labeling does not damage the DNA, it is possible to label the DNA densely and thus obtain high resolution. In an interesting application of this method, Grnwald et al (53) were able to type and identify bacteriophages based on an amplitude modulation profile in which the fluorescence intensity along the DNA molecules stretched over nanofluidic channels exhibited a unique molecular fingerprint (Figure 2C). …”

Section: Om In Microbiology: a New Perspectivementioning

confidence: 99%

Applications of Optical DNA Mapping in Microbiology

et al. 2017

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Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.

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Section: Om In Microbiology: a New Perspectivementioning

confidence: 99%

Applications of Optical DNA Mapping in Microbiology

et al. 2017

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“…The authors have also demonstrated that the use of super-resolution imaging techniques can improve resolution between fluorescent nicking sites to 100 bp 135 . They demonstrated the use of mapping as scaffolding to complete de novo sequence assembly of new genomes 136 , to finish particularly difficult and repetitive regions of the human genome 137 , to detect structural variations (insertions, deletions, and inversions) 138, 139 in an individual human genome 140 , and for strain typing of bacteriophages λ and T7 from a background phage library by covalently labeling at methyltransferase recognition sites 141 . Techniques for mapping epigenetic markers will be further discussed in Section 2.5.…”

Section: Assessment Modalitiesmentioning

confidence: 99%

Analysis of single nucleic acid molecules in micro- and nano-fluidics

2016

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Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano- fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano- fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano- structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

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“…In addition to genome assembly guidance, optical mapping offers a complementary approach for sequence variation analysis in large-region comparisons in addition to nucleotide matches and provides unique traits for evolutionary or functional analyses. At present, direct comparisons between optical maps are usually conducted in microbes but are lacking in large genomes, such as animals or plants [8]. Here, we present two optical Manis maps, and we reveal and compare their genetic structures using pairwise sequence alignments to identify their interspecific variations.…”

Section: Data Descriptionmentioning

confidence: 99%

Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica

Huang

Xiao

et al. 2016

GigaScience

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Background: The pangolin is a Pholidota mammal with large keratin scales protecting its skin. Two pangolin species (Manis pentadactyla and Manis javanica) have been recorded as critically endangered on the International Union for Conservation of Nature Red List of Threatened Species. Optical mapping constructs high-resolution restriction maps from single DNA molecules for genome analysis at the megabase scale and to assist genome assembly. Here, we constructed restriction maps of M. pentadactyla and M. javanica using optical mapping to assist with genome assembly and analysis of these species. Findings: Genomic DNA was nicked with Nt.BspQI and then labeled using fluorescently labeled bases that were detected by the Irys optical mapping system. In total, 3,313,734 DNA molecules (517.847 Gb) for M. pentadactyla and 3,439,885 DNA molecules (504.743 Gb) for M. javanica were obtained, which corresponded to approximately 178X and 177X genome coverage, respectively. Qualified molecules (≥150 kb with a label density of >6 sites per 100 kb) were analyzed using the de novo assembly program embedded in the IrysView pipeline. We obtained two maps that were 2.91 Gb and 2.85 Gb in size with N50s of 1.88 Mb and 1.97 Mb, respectively. Conclusions: Optical mapping reveals large-scale structural information that is especially important for non-model genomes that lack a good reference. The approach has the potential to guide de novo assembly of genomes sequenced using next-generation sequencing. Our data provide a resource for Manidae genome analysis and references for de novo assembly. This note also provides new insights into Manidae evolutionary analysis at the genome structure level.

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Bacteriophage strain typing by rapid single molecule analysis

Cited by 66 publications

References 38 publications

Applications of Optical DNA Mapping in Microbiology

Applications of Optical DNA Mapping in Microbiology

Analysis of single nucleic acid molecules in micro- and nano-fluidics

Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica

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