1
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Irving OJ, Matthews L, Coulthard S, Neely RK, Grant MM, Albrecht T. Sterically Enhanced Control of Enzyme-Assisted DNA Assembly. Chembiochem 2023; 24:e202300361. [PMID: 37681318 DOI: 10.1002/cbic.202300361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/15/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100 bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA that spatially restrict enzymatic activity. This approach, sterically controlled nuclease enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, when using the same starting materials, conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
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Affiliation(s)
- Oliver J Irving
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Lauren Matthews
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Steven Coulthard
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Melissa M Grant
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham and Birmingham Dental Hospital, Birmingham Community Healthcare Trust), 5 Mill Pool Way, Edgbaston, Birmingham, B5 7EG, UK
| | - Tim Albrecht
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
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2
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Peeters W, Toyouchi S, Fujita Y, Wolf M, Fortuni B, Fron E, Inose T, Hofkens J, Endo T, Miyata Y, Uji-i H. Remote Excitation of Tip-Enhanced Photoluminescence with a Parallel AgNW Coupler. ACS OMEGA 2023; 8:38386-38393. [PMID: 37867716 PMCID: PMC10586305 DOI: 10.1021/acsomega.3c04952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023]
Abstract
Tip-enhanced photoluminescence (TEPL) microscopy allows for the correlation of scanning probe microscopic images and photoluminescent spectra at the nanoscale level in a similar way to tip-enhanced Raman scattering (TERS) microscopy. However, due to the higher cross-section of fluorescence compared to Raman scattering, the diffraction-limited background signal generated by far-field excitation is a limiting factor in the achievable spatial resolution of TEPL. Here, we demonstrate a way to overcome this drawback by using remote excitation TEPL (RE-TEPL). With this approach, the excitation and detection positions are spatially separated, minimizing the far-field contribution. Two probe designs are evaluated, both experimentally and via simulations. The first system consists of gold nanoparticles (AuNPs) through photoinduced deposition on a silver nanowire (AgNW), and the second system consists of two offset parallel AgNWs. This latter coupler system shows a higher coupling efficiency and is used to successfully demonstrate RE-TEPL spectral mapping on a MoSe2/WSe2 lateral heterostructure to reveal spatial heterogeneity at the heterojunction.
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Affiliation(s)
- Wannes Peeters
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Shuichi Toyouchi
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Yasuhiko Fujita
- Research
Institute for Sustainable Chemistry, National
Institute of Advanced Industrial Science and Technology (AIST Chugoku), Kagamiyama 3-11-32, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Mathias Wolf
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Beatrice Fortuni
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Eduard Fron
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Tomoko Inose
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- The
HAKUBI Center for Advanced Research, Kyoto
University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Johan Hofkens
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
- Max
Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Takahiko Endo
- Department
of Physics, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yasumitsu Miyata
- Department
of Physics, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Hiroshi Uji-i
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- RIES, Hokkaido University, N20 W10, Kita-Ward, Sapporo 001-0020, Japan
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3
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Nogin Y, Bar-Lev D, Hanania D, Detinis Zur T, Ebenstein Y, Yaakobi E, Weinberger N, Shechtman Y. Design of optimal labeling patterns for optical genome mapping via information theory. Bioinformatics 2023; 39:btad601. [PMID: 37758248 PMCID: PMC10563147 DOI: 10.1093/bioinformatics/btad601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023] Open
Abstract
MOTIVATION Optical genome mapping (OGM) is a technique that extracts partial genomic information from optically imaged and linearized DNA fragments containing fluorescently labeled short sequence patterns. This information can be used for various genomic analyses and applications, such as the detection of structural variations and copy-number variations, epigenomic profiling, and microbial species identification. Currently, the choice of labeled patterns is based on the available biochemical methods and is not necessarily optimized for the application. RESULTS In this work, we develop a model of OGM based on information theory, which enables the design of optimal labeling patterns for specific applications and target organism genomes. We validated the model through experimental OGM on human DNA and simulations on bacterial DNA. Our model predicts up to 10-fold improved accuracy by optimal choice of labeling patterns, which may guide future development of OGM biochemical labeling methods and significantly improve its accuracy and yield for applications such as epigenomic profiling and cultivation-free pathogen identification in clinical samples. AVAILABILITY AND IMPLEMENTATION https://github.com/yevgenin/PatternCode.
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Affiliation(s)
- Yevgeni Nogin
- Russell Berrie Nanotechnology Institute, Technion, Haifa 320003, Israel
| | | | - Dganit Hanania
- Department of Computer Science, Technion, Haifa 320003, Israel
| | - Tahir Detinis Zur
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eitan Yaakobi
- Department of Computer Science, Technion, Haifa 320003, Israel
| | - Nir Weinberger
- Department of Electrical Engineering, Technion, Haifa 320003, Israel
| | - Yoav Shechtman
- Russell Berrie Nanotechnology Institute, Technion, Haifa 320003, Israel
- Department of Biomedical Engineering, Technion, Haifa 320003, Israel
- Lorry I. Lokey Center for Life Sciences and Engineering, Technion, Haifa 320003, Israel
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4
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Ceresa L, Chavez J, Bus MM, Budowle B, Kitchner E, Kimball J, Gryczynski I, Gryczynski Z. Multi intercalators FRET enhanced detection of minute amounts of DNA. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:593-605. [PMID: 37140595 DOI: 10.1007/s00249-023-01655-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/15/2023] [Indexed: 05/05/2023]
Abstract
A novel approach is presented that increases sensitivity and specificity for detecting minimal traces of DNA in liquid and on solid samples. Förster Resonance Energy Transfer (FRET) from YOYO to Ethidium Bromide (EtBr) substantially increases the signal from DNA-bound EtBr highly enhancing sensitivity and specificity for DNA detection. The long fluorescence lifetime of the EtBr acceptor, when bound to DNA, allows for multi-pulse pumping with time gated (MPPTG) detection, which highly increases the detectable signal of DNA-bound EtBr. A straightforward spectra/image subtraction eliminates sample background and allows for a huge increase in the overall detection sensitivity. Using a combination of FRET and MPPTG detection an amount as small as 10 pg of DNA in a microliter sample can be detected without any additional sample purification/manipulation or use of amplification technologies. This amount of DNA is comparable to the DNA content of a one to two human cells. Such a detection method based on simple optics opens the potential for robust, highly sensitive DNA detection/imaging in the field, quick evaluation/sorting (i.e., triaging) of collected DNA samples, and can support various diagnostic assays.
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Affiliation(s)
- Luca Ceresa
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA.
| | - Jose Chavez
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Magdalena M Bus
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA
| | - Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Science Institute, Radford University, Radford, VA, USA
| | - Emma Kitchner
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Ignacy Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, 76109, USA
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5
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Hasing T, Bombarely A. Genomic Approaches for the Study of Flower Development in Floriculture Crops. Methods Mol Biol 2023; 2686:453-494. [PMID: 37540373 DOI: 10.1007/978-1-0716-3299-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The advances in genomics and bioinformatics have made possible the study in non-model plants of phenotypes associated to flower development. Floriculture crops are an interesting source of traits associated to flower development such as the transition between zygomorphic and actinomorphic flowers or the production of flowers with double and triple corollas. In this chapter, we summarize the material and methods for the use of floriculture crops to study flower development using genomic tools, from the sequencing and assembly of a reference genome to QTL and RNA-Seq analysis to search candidate genes associated to specific traits.
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Affiliation(s)
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (UPV-CSIC), Valencia, Spain.
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6
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Zhang T, Zhou J, Gao W, Jia Y, Wei Y, Wang G. Complex genome assembly based on long-read sequencing. Brief Bioinform 2022; 23:6657663. [PMID: 35940845 DOI: 10.1093/bib/bbac305] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 07/06/2022] [Indexed: 11/12/2022] Open
Abstract
High-quality genome chromosome-scale sequences provide an important basis for genomics downstream analysis, especially the construction of haplotype-resolved and complete genomes, which plays a key role in genome annotation, mutation detection, evolutionary analysis, gene function research, comparative genomics and other aspects. However, genome-wide short-read sequencing is difficult to produce a complete genome in the face of a complex genome with high duplication and multiple heterozygosity. The emergence of long-read sequencing technology has greatly improved the integrity of complex genome assembly. We review a variety of computational methods for complex genome assembly and describe in detail the theories, innovations and shortcomings of collapsed, semi-collapsed and uncollapsed assemblers based on long reads. Among the three methods, uncollapsed assembly is the most correct and complete way to represent genomes. In addition, genome assembly is closely related to haplotype reconstruction, that is uncollapsed assembly realizes haplotype reconstruction, and haplotype reconstruction promotes uncollapsed assembly. We hope that gapless, telomere-to-telomere and accurate assembly of complex genomes can be truly routinely achieved using only a simple process or a single tool in the future.
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Affiliation(s)
- Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Jie Zhou
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Wentao Gao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuran Jia
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yanan Wei
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
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7
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Ceresa L, Chavez J, Bus MM, Budowle B, Kitchner E, Kimball J, Gryczynski I, Gryczynski Z. Förster Resonance Energy Transfer-Enhanced Detection of Minute Amounts of DNA. Anal Chem 2022; 94:5062-5068. [PMID: 35286067 DOI: 10.1021/acs.analchem.1c05275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article presents a novel approach to increase the detection sensitivity of trace amounts of DNA in a sample by employing Förster resonance energy transfer (FRET) between intercalating dyes. Two intercalators that present efficient FRET were used to enhance sensitivity and improve specificity in detecting minute amounts of DNA. Comparison of steady-state acceptor emission spectra with and without the donor allows for simple and specific detection of DNA (acceptor bound to DNA) down to 100 pg/μL. When utilizing as an acceptor a dye with a significantly longer lifetime (e.g., ethidium bromide bound to DNA), multipulse pumping and time-gated detection enable imaging/visualization of picograms of DNA present in a microliter of an unprocessed sample or DNA collected on a swab or other substrate materials.
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Affiliation(s)
- Luca Ceresa
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Jose Chavez
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Magdalena M Bus
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States.,Department of Microbiology, Immunology & Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States.,Department of Microbiology, Immunology & Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States
| | - Emma Kitchner
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Ignacy Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
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8
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Torstensson E, Goyal G, Johnning A, Westerlund F, Ambjörnsson T. Combining dense and sparse labeling in optical DNA mapping. PLoS One 2021; 16:e0260489. [PMID: 34843574 PMCID: PMC8629184 DOI: 10.1371/journal.pone.0260489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.
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Affiliation(s)
- Erik Torstensson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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9
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Wittmeyer KT, Oppenheim SJ, Hopper KR. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage. G3 (BETHESDA, MD.) 2021; 12:6423991. [PMID: 34751385 PMCID: PMC8727961 DOI: 10.1093/g3journal/jkab386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies of A. atriplicis made with Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies of A. atriplicis differed in contiguity, and the meta-assembly of these assemblies was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly to the point where it was also at the chromosomal-level. However, completeness of the A. atriplicis assembly, as measured by percent complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportions with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by percent complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggest greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.
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Affiliation(s)
- Kameron T Wittmeyer
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA
| | | | - Keith R Hopper
- USDA-ARS, Beneficial Insect Introductions Research Unit, Newark, DE 19713, USA,Corresponding author: USDA-ARS, Beneficial Insect Introductions Research Unit, 501 South Chapel Street, Newark, DE 19713, USA.
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10
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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11
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Chen K, Gularek F, Liu B, Weinhold E, Keyser UF. Electrical DNA Sequence Mapping Using Oligodeoxynucleotide Labels and Nanopores. ACS NANO 2021; 15:2679-2685. [PMID: 33478224 PMCID: PMC7905879 DOI: 10.1021/acsnano.0c07947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Identifying DNA species is crucial for diagnostics. For DNA identification, single-molecule DNA sequence mapping is an alternative to DNA sequencing toward fast point-of-care testing, which traditionally relies on targeting and labeling DNA sequences with fluorescent labels and readout using optical imaging methods. A nanopore is a promising sensor as a complement to optical mapping with advantages of electric measurement suitable for portable devices and potential for high resolution. Here, we demonstrate a high-resolution nanopore-based DNA sequence mapping by labeling specific short sequence motifs with oligodeoxynucleotides (ODNs) using DNA methyltransferase (MTase) and detecting them using nanopores. We successfully detected ODNs down to the size of 11 nucleotides without introducing extra reporters and resolved neighboring sites with a distance of 141 bp (∼48 nm) on a single DNA molecule. To accurately locate the sequence motif positions on DNA, a nanopore data analysis method is proposed by considering DNA velocity change through nanopores and using ensemble statistics to translate the time-dependent signals to the location information. Our platform enables high-resolution detection of small labels on DNA and high-accuracy localization of them for DNA species identification in an all-electrical format. The method presents an alternative to optical techniques relying on fluorescent labels and is promising for miniature-scale integration for diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Boyao Liu
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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12
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Bhattacharjee G, Gohil N, Lam NL, Singh V. CRISPR-based diagnostics for detection of pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:45-57. [PMID: 34127201 DOI: 10.1016/bs.pmbts.2021.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The improved sensitivity and superior specificity associated with the use of molecular assays has improved the fate of disease diagnosis by bestowing the clinicians with outcomes that are both rapid and precise. In recent years, CRISPR has made considerable progress in in vitro diagnostic platform which has paved its way for developing rapid and sensitive CRISPR-based diagnostic tools. Improved perception and better understanding of diverse CRISPR-Cas systems has broadened the reach of CRISPR applications for not just early detection of pathogens but also for early onset of diseases such as cancer. The inherent allele specificity of CRISPR is the predominant reason for its application in designing a diagnostic-tool that is field-deployable, portable, sensitive, specific and rapid. In this chapter, we highlight various CRISPR-based diagnostic platforms, its applications, challenges and future prospects of the CRISPR-Cas system.
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Affiliation(s)
- Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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13
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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14
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Mukherjee K, Alipanahi B, Kahveci T, Salmela L, Boucher C. Aligning optical maps to de Bruijn graphs. Bioinformatics 2020; 35:3250-3256. [PMID: 30698651 DOI: 10.1093/bioinformatics/btz069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/31/2018] [Accepted: 01/25/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps-called Rmaps, or for aligning optical maps to assembled reads. However, the problem of aligning an Rmap to a graph representing the sequence data of the same genome has not been studied before. Such an alignment provides a mapping between two sets of data: optical maps and sequence data which will facilitate the usage of optical maps in the sequence assembly step itself. RESULTS We define the problem of aligning an Rmap to a de Bruijn graph and present the first algorithm for solving this problem which is based on a seed-and-extend approach. We demonstrate that our method is capable of aligning 73% of Rmaps generated from the Escherichia coli genome to the de Bruijn graph constructed from short reads generated from the same genome. We validate the alignments and show that our method achieves an accuracy of 99.6%. We also show that our method scales to larger genomes. In particular, we show that 76% of Rmaps can be aligned to the de Bruijn graph in the case of human data. AVAILABILITY AND IMPLEMENTATION The software for aligning optical maps to de Bruijn graph, omGraph is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/omGraph. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kingshuk Mukherjee
- Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, USA
| | - Bahar Alipanahi
- Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, USA
| | - Tamer Kahveci
- Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, USA
| | - Leena Salmela
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, College of Engineering, University of Florida, Gainesville, USA
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15
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Müller V, Nyblom M, Johnning A, Wrande M, Dvirnas A, KK S, Giske CG, Ambjörnsson T, Sandegren L, Kristiansson E, Westerlund F. Cultivation-Free Typing of Bacteria Using Optical DNA Mapping. ACS Infect Dis 2020; 6:1076-1084. [PMID: 32294378 PMCID: PMC7304876 DOI: 10.1021/acsinfecdis.9b00464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 01/06/2023]
Abstract
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - My Nyblom
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers
Centre, Chalmers Science
Park, 412 88 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Marie Wrande
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Sriram KK
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska
Institutet, Alfred Nobels
Allé 8, 141 86 Stockholm, Sweden
- Department of Clinical
Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Linus Sandegren
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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16
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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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17
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Wand NO, Smith DA, Wilkinson AA, Rushton AE, Busby SJW, Styles IB, Neely RK. DNA barcodes for rapid, whole genome, single-molecule analyses. Nucleic Acids Res 2020; 47:e68. [PMID: 30918971 PMCID: PMC6614835 DOI: 10.1093/nar/gkz212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
We report an approach for visualizing DNA sequence and using these ‘DNA barcodes’ to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.
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Affiliation(s)
- Nathaniel O Wand
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,Physical Sciences of Imaging in the Biomedical Sciences Centre for Doctoral Training, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Darren A Smith
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew A Wilkinson
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ashleigh E Rushton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Iain B Styles
- School of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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18
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Goyvaerts V, Van Snick S, D'Huys L, Vitale R, Helmer Lauer M, Wang S, Leen V, Dehaen W, Hofkens J. Fluorescent SAM analogues for methyltransferase based DNA labeling. Chem Commun (Camb) 2020; 56:3317-3320. [DOI: 10.1039/c9cc08938a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this work, the preparation of new S-adenosyl-l-methionine (SAM) analogues for sequence specific DNA labeling is evaluated. Fluorescent cofactors were synthesized and their applicability in methyltransferase based optical mapping is demonstrated.
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Affiliation(s)
- Vince Goyvaerts
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Sven Van Snick
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Laurens D'Huys
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Raffaele Vitale
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Milena Helmer Lauer
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Su Wang
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Volker Leen
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Wim Dehaen
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Johan Hofkens
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
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19
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Cao M, Xu K, Yu X, Bi G, Liu Y, Kong F, Sun P, Tang X, Du G, Ge Y, Wang D, Mao Y. A chromosome-level genome assembly of Pyropia haitanensis (Bangiales, Rhodophyta). Mol Ecol Resour 2020; 20:216-227. [PMID: 31600851 PMCID: PMC6972535 DOI: 10.1111/1755-0998.13102] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 01/07/2023]
Abstract
Pyropia haitanensis (Bangiales, Rhodophyta), a major economically important marine crop, is also considered as an ideal research model of Rhodophyta to address several major biological questions such as sexual reproduction and adaptation to intertidal abiotic stresses. However, comparative genomic analysis to decipher the underlying molecular mechanisms is hindered by the lack of high-quality genome information. Therefore, we integrated sequencing data from Illumina short-read sequencing, PacBio single-molecule sequencing and BioNano optical genome mapping. The assembled genome was approximately 53.3 Mb with an average GC% of 67.9%. The contig N50 and scaffold N50 were 510.3 kb and 5.8 Mb, respectively. Additionally, 10 superscaffolds representing 80.9% of the total assembly (42.7 Mb) were anchored and orientated to the 5 linkage groups based on markers and genetic distance; this outcome is consistent with the karyotype of five chromosomes (n = 5) based on cytological observation in P. haitanensis. Approximately 9.6% and 14.6% of the genomic region were interspersed repeat and tandem repeat elements, respectively. Based on full-length transcriptome data generated by PacBio, 10,903 protein-coding genes were identified. The construction of a genome-wide phylogenetic tree demonstrated that the divergence time of P. haitanensis and Porphyra umbilicalis was ~204.4 Ma. Interspecies comparison revealed that 493 gene families were expanded and that 449 were contracted in the P. haitanensis genome compared with those in the Po. umbilicalis genome. The genome identified is of great value for further research on the genome evolution of red algae and genetic adaptation to intertidal stresses.
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Affiliation(s)
- Min Cao
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Kuipeng Xu
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Guiqi Bi
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yang Liu
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Peipei Sun
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Guoying Du
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yuan Ge
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (OUC)Ministry of EducationQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University)Ministry of EducationSanyaChina
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20
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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21
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Chen P, Jing X, Ren J, Cao H, Hao P, Li X. Modelling BioNano optical data and simulation study of genome map assembly. Bioinformatics 2019; 34:3966-3974. [PMID: 29893801 PMCID: PMC6247929 DOI: 10.1093/bioinformatics/bty456] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/07/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation The launch of the BioNano next-generation mapping system has greatly enhanced the performance of physical map construction, thus rapidly expanding the application of optical mapping in genome research. Data biases have profound implications for downstream applications. However, very little is known about the properties and biases of BioNano data, and the very factors that contribute to whole-genome optical map assembly. Results We generated BioNano molecule data from eight organisms with diverse base compositions. We first characterized the properties/biases of BioNano molecule data, i.e. molecule length distribution, false labelling signal, variation of optical resolution and coverage distribution bias, and their inducing factors such as chimeric molecules, fragile sites and DNA molecule stretching. Second, we developed the BioNano Molecule SIMulator (BMSIM), a novel computer simulation program for optical data. BMSIM, is of great use for future genome mapping projects. Third, we evaluated the experimental variables that impact whole-genome optical map assembly. Specifically, the effects of coverage depth, molecule length, false-positive and false-negative labelling signals, chimeric molecules and nicking enzyme and nick site density were investigated. Our simulation study provides the empirical findings on how to control experimental variables and gauge analytical parameters to maximize benefit and minimize cost on whole-genome optical map assembly. Availability and implementation BMSIM is freely available on: https://github.com/pingchen09990102/BMSIM. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jian Ren
- Ultravision Technology, Beijing, China
| | - Han Cao
- BioNano Genomics, San Diego, CA, USA
| | - Pei Hao
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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22
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Deen J, Wang S, Van Snick S, Leen V, Janssen K, Hofkens J, Neely RK. A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA. Nucleic Acids Res 2019; 46:e64. [PMID: 29546351 PMCID: PMC6009647 DOI: 10.1093/nar/gky184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.
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Affiliation(s)
- Jochem Deen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Su Wang
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Sven Van Snick
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Volker Leen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kris Janssen
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Laboratory of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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23
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Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. ACTA ACUST UNITED AC 2019; 122:e59. [PMID: 29851291 DOI: 10.1002/cpmb.59] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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24
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Ruvinskiy D, Larkin DM, Farré M. A Near Chromosome Assembly of the Dromedary Camel Genome. Front Genet 2019; 10:32. [PMID: 30804979 PMCID: PMC6371769 DOI: 10.3389/fgene.2019.00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/17/2019] [Indexed: 01/11/2023] Open
Abstract
The dromedary camel is an economically and socially important species of livestock in many parts of the world, being used for transport and the production of milk and meat. Much like cattle and horses, the camel may be found in industrial farming conditions as well as used in sporting. Camel racing is a multi-million dollar industry, with some specimens being valued at upward of 9.5 million USD. Despite its apparent value to humans, the dromedary camel is a neglected species in genomics. While cattle and other domesticated species have had much attention in terms of genome assembly, the camel has only been assembled to scaffold level, which does not give a clear indication of the order or chromosomal location of sequenced fragments. In this study, the Reference Assistant Chromosome Assembly (RACA) algorithm was implemented to use read-pair information of camel scaffolds, aligned with the cattle and human genomes in order to organize and orient these scaffolds in a near-chromosome level assembly. This method generated 72 large size fragments (N50 54.36 Mb). These predicted chromosome fragments (PCFs) were then compared with comparative maps of camel and cytogenetic map of alpaca chromosomes, allowing us to further upgrade the assembly. This dromedary camel assembly will be an invaluable tool to verify future camel assemblies generated with chromatin conformation or/and long read technologies. This study provides the first near-chromosome assembly of the dromedary camel, thus adding this economically important species to a growing pool of knowledge regarding the genome structure of domesticated livestock.
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Affiliation(s)
- Daniil Ruvinskiy
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom
| | - Denis M Larkin
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,The Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marta Farré
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, United Kingdom.,School of Biosciences, University of Kent, Canterbury, United Kingdom
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25
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Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA. Molecules 2019; 24:molecules24030491. [PMID: 30704053 PMCID: PMC6384704 DOI: 10.3390/molecules24030491] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 11/29/2022] Open
Abstract
The ability to watch single molecules of DNA has revolutionised how we study biological transactions concerning nucleic acids. Many strategies have been developed to manipulate DNA molecules to investigate mechanical properties, dynamics and protein–DNA interactions. Imaging methods using small molecules and protein-based probes to visualise DNA have propelled our understanding of complex biochemical reactions involving DNA. This review focuses on summarising some of the methodological developments made to visualise individual DNA molecules and discusses how these probes have been used in single-molecule biophysical assays.
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26
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Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
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Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
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27
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Abstract
Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
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Affiliation(s)
- Pranav Agrawal
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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28
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Panfilio KA, Angelini DR. By land, air, and sea: hemipteran diversity through the genomic lens. CURRENT OPINION IN INSECT SCIENCE 2018; 25:106-115. [PMID: 29602356 DOI: 10.1016/j.cois.2017.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/15/2017] [Indexed: 06/08/2023]
Abstract
Thanks to a recent spate of sequencing projects, the Hemiptera are the first hemimetabolous insect order to achieve a critical mass of species with sequenced genomes, establishing the basis for comparative genomics of the bugs. However, as the most speciose hemimetabolous order, there is still a vast swathe of the hemipteran phylogeny that awaits genomic representation across subterranean, terrestrial, and aquatic habitats, and with lineage-specific and developmentally plastic cases of both wing polyphenisms and flightlessness. In this review, we highlight opportunities for taxonomic sampling beyond obvious pest species candidates, motivated by intriguing biological features of certain groups as well as the rich research tradition of ecological, physiological, developmental, and particularly cytogenetic investigation that spans the diversity of the Hemiptera.
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Affiliation(s)
- Kristen A Panfilio
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom; Institute of Zoology: Developmental Biology, University of Cologne, 50674 Cologne, Germany.
| | - David R Angelini
- Department of Biology, Colby College, Waterville, ME 04901, United States
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29
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Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA.
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30
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Łopacińska-Jørgensen JM, Pedersen JN, Bak M, Mehrjouy MM, Sørensen KT, Østergaard PF, Bilenberg B, Kristensen A, Taboryski RJ, Flyvbjerg H, Marie R, Tommerup N, Silahtaroglu A. Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing. Sci Rep 2017; 7:17893. [PMID: 29263336 PMCID: PMC5738345 DOI: 10.1038/s41598-017-18091-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022] Open
Abstract
Next-generation sequencing (NGS) has caused a revolution, yet left a gap: long-range genetic information from native, non-amplified DNA fragments is unavailable. It might be obtained by optical mapping of megabase-sized DNA molecules. Frequently only a specific genomic region is of interest, so here we introduce a method for selection and enrichment of megabase-sized DNA molecules intended for single-molecule optical mapping: DNA from a human cell line is digested by the NotI rare-cutting enzyme and size-selected by pulsed-field gel electrophoresis. For demonstration, more than 600 sub-megabase- to megabase-sized DNA molecules were recovered from the gel and analysed by denaturation-renaturation optical mapping. Size-selected molecules from the same gel were sequenced by NGS. The optically mapped molecules and the NGS reads showed enrichment from regions defined by NotI restriction sites. We demonstrate that the unannotated genome can be characterized in a locus-specific manner via molecules partially overlapping with the annotated genome. The method is a promising tool for investigation of structural variants in enriched human genomic regions for both research and diagnostic purposes. Our enrichment method could potentially work with other genomes or target specified regions by applying other genomic editing tools, such as the CRISPR/Cas9 system.
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Affiliation(s)
- Joanna M Łopacińska-Jørgensen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Mads Bak
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Mana M Mehrjouy
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Kristian T Sørensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Peter F Østergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Brian Bilenberg
- NIL Technology ApS, Diplomvej 381, Kongens Lyngby, 2800, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Rafael J Taboryski
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads 345a, Kongens Lyngby, 2800, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Copenhagen, 2200, Denmark.
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31
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Chen K, Juhasz M, Gularek F, Weinhold E, Tian Y, Keyser UF, Bell NAW. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores. NANO LETTERS 2017; 17:5199-5205. [PMID: 28829136 PMCID: PMC5599873 DOI: 10.1021/acs.nanolett.7b01009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Yu Tian
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail:
| | - Nicholas A. W. Bell
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail: . Fax: +44 (0)1223 337000
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32
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Abstract
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.
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33
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Abstract
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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34
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Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding. Genetics 2017; 206:1237-1250. [PMID: 28468906 PMCID: PMC5500127 DOI: 10.1534/genetics.117.200303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultradense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/bacterial-artificial-chromosome clone pools, and by restriction site-associated DNA sequencing of these clone pools to produce an ultradense whole-genome restriction map to facilitate genome scaffolding. A bootstrap-based minimum spanning tree algorithm is developed for grouping and ordering of genome-wide markers and is implemented in a user-friendly, integrated software package (AMMO). We perform extensive analyses to validate the power and accuracy of our approach in the model plant Arabidopsis thaliana and human. We also demonstrate the utility of RadMap for enhancing the contiguity of a variety of whole-genome shotgun assemblies generated using either short Illumina reads (300 bp) or long PacBio reads (6-14 kb), with up to 15-fold improvement of N50 (∼816 kb-3.7 Mb) and high scaffolding accuracy (98.1-98.5%). RadMap outperforms BioNano and Hi-C when input assembly is highly fragmented (contig N50 = 54 kb). RadMap can capture wide-range contiguity information and provide an efficient and flexible tool for high-resolution physical mapping and scaffolding of highly fragmented assemblies.
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35
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Methyltransferase-Directed Labeling of Biomolecules and its Applications. Angew Chem Int Ed Engl 2017; 56:5182-5200. [PMID: 27943567 PMCID: PMC5502580 DOI: 10.1002/anie.201608625] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 01/01/2023]
Abstract
Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.
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Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale BiologySchool of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM)Station 17CH-1015LausanneSwitzerland
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Robert K. Neely
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
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36
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Die Methyltransferase-gesteuerte Markierung von Biomolekülen und ihre Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale Biology; School of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM); Station 17 CH-1015 Lausanne Schweiz
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Robert K. Neely
- School of Chemistry; University of Birmingham; Edgbaston Birmingham B15 2TT Großbritannien
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
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37
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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38
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Müller V, Westerlund F. Optical DNA mapping in nanofluidic devices: principles and applications. LAB ON A CHIP 2017; 17:579-590. [PMID: 28098301 DOI: 10.1039/c6lc01439a] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Microfluidic DNA Stretching Device for Single-Molecule Diagnostics. Methods Mol Biol 2017. [PMID: 28044290 DOI: 10.1007/978-1-4939-6734-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The method described here enables the automatic stretching and patterning of single DNA molecules onto a solid surface. It does not require chemical modification of the DNA or surface modification of the substrate. To detect a signal variation caused by sequence-specific dye binding or partial melting, it is crucial that the DNA molecules are arrayed in a parallel direction inside the narrow microscopic field. The method uses zigzag-shaped microgrooves in a densely-arranged molecular patterning apparatus in a microfluidic channel. By syringing through the microchannel, over 1500 DNA molecules can be arrayed simultaneously in the microgrooves. It will therefore serve as a template preparation for DNA molecular diagnosis by high-resolution imaging.
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40
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Healey KR, Jimenez Ortigosa C, Shor E, Perlin DS. Genetic Drivers of Multidrug Resistance in Candida glabrata. Front Microbiol 2016; 7:1995. [PMID: 28018323 PMCID: PMC5156712 DOI: 10.3389/fmicb.2016.01995] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/29/2016] [Indexed: 12/31/2022] Open
Abstract
Both the incidence of invasive fungal infections and rates of multidrug resistance associated with fungal pathogen Candida glabrata have increased in recent years. In this perspective, we will discuss the mechanisms underlying the capacity of C. glabrata to rapidly develop resistance to multiple drug classes, including triazoles and echinocandins. We will focus on the extensive genetic diversity among clinical isolates of C. glabrata, which likely enables this yeast to survive multiple stressors, such as immune pressure and antifungal exposure. In particular, over half of C. glabrata clinical strains collected from U.S. and non-U.S. sites have mutations in the DNA mismatch repair gene MSH2, leading to a mutator phenotype and increased frequencies of drug-resistant mutants in vitro. Furthermore, recent studies and data presented here document extensive chromosomal rearrangements among C. glabrata strains, resulting in a large number of distinct karyotypes within a single species. By analyzing clonal, serial isolates derived from individual patients treated with antifungal drugs, we were able to document chromosomal changes occurring in C. glabrata in vivo during the course of antifungal treatment. Interestingly, we also show that both MSH2 genotypes and chromosomal patterns cluster consistently into specific strain types, indicating that C. glabrata has a complex population structure where genomic variants arise, perhaps during the process of adaptation to environmental changes, and persist over time.
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Affiliation(s)
- Kelley R Healey
- Public Health Research Institute, Rutgers Biomedical and Health Sciences, New Jersey Medical School Newark, NJ, USA
| | - Cristina Jimenez Ortigosa
- Public Health Research Institute, Rutgers Biomedical and Health Sciences, New Jersey Medical School Newark, NJ, USA
| | - Erika Shor
- Public Health Research Institute, Rutgers Biomedical and Health Sciences, New Jersey Medical School Newark, NJ, USA
| | - David S Perlin
- Public Health Research Institute, Rutgers Biomedical and Health Sciences, New Jersey Medical School Newark, NJ, USA
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41
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Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping. Sci Rep 2016; 6:37938. [PMID: 27905467 PMCID: PMC5131345 DOI: 10.1038/srep37938] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/01/2016] [Indexed: 12/03/2022] Open
Abstract
Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrika Rajer
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saair Quaderi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Henkin G, Berard D, Stabile F, Shayegan M, Leith JS, Leslie SR. Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces. Anal Chem 2016; 88:11100-11107. [DOI: 10.1021/acs.analchem.6b03149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Gil Henkin
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Daniel Berard
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Francis Stabile
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Marjan Shayegan
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Jason S. Leith
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, Quebec, Canada H3A 2T8
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Chaney L, Sharp AR, Evans CR, Udall JA. Genome Mapping in Plant Comparative Genomics. TRENDS IN PLANT SCIENCE 2016; 21:770-780. [PMID: 27289181 DOI: 10.1016/j.tplants.2016.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/10/2023]
Abstract
Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.
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Affiliation(s)
- Lindsay Chaney
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Aaron R Sharp
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Carrie R Evans
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA.
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Shuang B, Wang W, Shen H, Tauzin LJ, Flatebo C, Chen J, Moringo NA, Bishop LDC, Kelly KF, Landes CF. Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions. Sci Rep 2016; 6:30826. [PMID: 27488312 PMCID: PMC4973222 DOI: 10.1038/srep30826] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/11/2016] [Indexed: 01/17/2023] Open
Abstract
Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.
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Affiliation(s)
- Bo Shuang
- Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | - Hao Shen
- Department of Chemistry, Rice University, Houston, TX 77251, USA
| | | | | | - Jianbo Chen
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | | | | | - Kevin F. Kelly
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, TX 77251, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
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45
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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules. Sci Rep 2016; 6:30410. [PMID: 27460437 PMCID: PMC4961956 DOI: 10.1038/srep30410] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 07/05/2016] [Indexed: 11/08/2022] Open
Abstract
The rapid spread of antibiotic resistance – currently one of the greatest threats to human health according to WHO – is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.
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Müller V, Karami N, Nyberg LK, Pichler C, Torche Pedreschi PC, Quaderi S, Fritzsche J, Ambjörnsson T, Åhrén C, Westerlund F. Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping. ACS Infect Dis 2016; 2:322-8. [PMID: 27627201 DOI: 10.1021/acsinfecdis.6b00017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Resistance to life-saving antibiotics increases rapidly worldwide, and multiresistant bacteria have become a global threat to human health. Presently, the most serious threat is the increasing spread of Enterobacteriaceae carrying genes coding for extended spectrum β-lactamases (ESBL) and carbapenemases on highly mobile plasmids. We here demonstrate how optical DNA maps of single plasmids can be used as fingerprints to trace plasmids, for example, during resistance outbreaks. We use the assay to demonstrate a potential transmission route of an ESBL-carrying plasmid between bacterial strains/species and between patients, during a polyclonal outbreak at a neonatal ward at Sahlgrenska University Hospital (Gothenburg, Sweden). Our results demonstrate that optical DNA mapping is an easy and rapid method for detecting the spread of plasmids mediating resistance. With the increasing prevalence of multiresistant bacteria, diagnostic tools that can aid in solving ongoing routes of transmission, in particular in hospital settings, will be of paramount importance.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, Guldhedsgatan 10, 41346 Gothenburg, Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Christoffer Pichler
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 22362 Lund, Sweden
| | - Paola C. Torche Pedreschi
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 22362 Lund, Sweden
| | - Saair Quaderi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 22362 Lund, Sweden
| | - Joachim Fritzsche
- Department of Applied
Physics, Chalmers University of Technology, Kemivägen 9, 41296 Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 22362 Lund, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, Guldhedsgatan 10, 41346 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
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Mariano DCB, Sousa TDJ, Pereira FL, Aburjaile F, Barh D, Rocha F, Pinto AC, Hassan SS, Saraiva TDL, Dorella FA, de Carvalho AF, Leal CAG, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002. BMC Genomics 2016; 17:315. [PMID: 27129708 PMCID: PMC4851793 DOI: 10.1186/s12864-016-2673-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/22/2016] [Indexed: 12/13/2022] Open
Abstract
Background Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements. Results In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions. Conclusion In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego César Batista Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Luiz Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, 721172, India
| | - Flávia Rocha
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Anne Cybelle Pinto
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Syed Shah Hassan
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Tessália Diniz Luerce Saraiva
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Alves Dorella
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Alex Fiorini de Carvalho
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Augusto Gomes Leal
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique César Pereira Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Vasco Ariston Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
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Pedersen JN, Marie R, Kristensen A, Flyvbjerg H. How to determine local stretching and tension in a flow-stretched DNA molecule. Phys Rev E 2016; 93:042405. [PMID: 27176327 DOI: 10.1103/physreve.93.042405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/07/2022]
Abstract
We determine the nonuniform stretching of and tension in a mega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA-e.g., native DNA extracted from human cells or bacteria-must be stretched with ease for inspection, this method applies.
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Affiliation(s)
- Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345B, DK-2800 Kongens Lyngby, Denmark
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Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury JM, Alberti A, Carreel F, D'Hont A. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics 2016; 17:243. [PMID: 26984673 PMCID: PMC4793746 DOI: 10.1186/s12864-016-2579-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 03/08/2016] [Indexed: 12/04/2022] Open
Abstract
Background Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). Results We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. Conclusion The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2579-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Gaëtan Droc
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Andrzej Kilian
- Diversity Arrays Technology, Yarralumla, Australian Capital Territory, 2600, Australia
| | - Alex Hastie
- BioNano Genomics, 9640 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Cremieux, BP5706, 91057, Evry, France
| | - Françoise Carreel
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France
| | - Angélique D'Hont
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398, Montpellier, cedex 5, France.
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Fu D, Mason AS, Xiao M, Yan H. Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:37-46. [PMID: 26566823 DOI: 10.1016/j.plantsci.2015.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 09/10/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
Compared to diploid species, allopolyploid crop species possess more complex genomes, higher productivity, and greater adaptability to changing environments. Next generation sequencing techniques have produced high-density genetic maps, whole genome sequences, transcriptomes and epigenomes for important polyploid crops. However, several problems interfere with the full application of next generation sequencing techniques to these crops. Firstly, different types of genomic variation affect sequence assembly and QTL mapping. Secondly, duplicated or homoeologous genes can diverge in function and then lead to emergence of many minor QTL, which increases difficulties in fine mapping, cloning and marker assisted selection. Thirdly, repetitive DNA sequences arising in polyploid crop genomes also impact sequence assembly, and are increasingly being shown to produce small RNAs to regulate gene expression and hence phenotypic traits. We propose that these three key features should be considered together when analyzing polyploid crop genomes. It is apparent that dissection of genomic structural variation, elucidation of the function and mechanism of interaction of homoeologous genes, and investigation of the de novo roles of repeat sequences in agronomic traits are necessary for genomics-based crop breeding in polyploids.
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Affiliation(s)
- Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hui Yan
- Key Laboratory of Poyang Lake Basin Agricultural Resources and Ecology of Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China
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