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Sousa TDJ, Parise D, Profeta R, Parise MTD, Gomide ACP, Kato RB, Pereira FL, Figueiredo HCP, Ramos R, Brenig B, Costa da Silva ALD, Ghosh P, Barh D, Góes-Neto A, Azevedo V. Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes. Sci Rep 2019; 9:16387. [PMID: 31705053 PMCID: PMC6841979 DOI: 10.1038/s41598-019-52695-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 10/18/2019] [Indexed: 12/29/2022] Open
Abstract
The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
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Affiliation(s)
- Thiago de Jesus Sousa
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Doglas Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Profeta
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Anne Cybelle Pinto Gomide
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Bentos Kato
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Luiz Pereira
- National Reference Laboratory for Aquatic Animal Diseases (AQUACEN) of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique Cesar Pereira Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases (AQUACEN) of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rommel Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University Göttingen, Göttingen, Germany
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, United States
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri West Bengal, India
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Whole-genome sequence of purple non-sulfur bacteria, Rhodobacter sphaeroides strain MBTLJ-8 with improved CO2 reduction capacity. J Biotechnol 2018; 288:9-14. [DOI: 10.1016/j.jbiotec.2018.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 01/13/2023]
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3
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Yadav H, Sharma P. A simple and novel DNA combing methodology for Fiber-FISH and optical mapping. Genomics 2018; 111:567-578. [PMID: 29550497 DOI: 10.1016/j.ygeno.2018.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 02/02/2023]
Abstract
Single molecule analysis can help us study genomics efficiently. It involves studying single DNA molecules for genomic studies. DNA combing is one of such techniques which allowed us to study single DNA molecules for multiple uses. DNA combing technology can be used to perform Fiber-FISH and optical mapping. Physical mapping of genomes can be studied by restriction digestion of combed DNA on glass slides. Restriction fragments can be arranged into optical maps by gathering fluorescent intensity data by CCD camera and image analysis by softwares. Physical mapping and DNA segment rearrangements can be studied by Fiber-FISH which involves application of probes on genomic DNA combed over glass slides. We developed a novel methodology involving combing solution optimization, denatured combed DNA and performed restriction digestion of combed DNA. Thus we provided an efficient and robust combing platform for its application in Fiber-FISH and optical mapping.
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Affiliation(s)
- Hemendra Yadav
- Department of Botany, University of Rajasthan, Jaipur, India.
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Maschmann A, Masters C, Davison M, Lallman J, Thompson D, Kounovsky-Shafer KL. Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes. J Vis Exp 2018. [PMID: 29443093 DOI: 10.3791/57141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Visualization of DNA for fluorescence microscopy utilizes a variety of dyes such as cyanine dyes. These dyes are utilized due to their high affinity and sensitivity for DNA. In order to determine if the DNA molecules are full length after the completion of the experiment, a method is required to determine if the stained molecules are full length by digesting DNA with restriction enzymes. However, stained DNA may inhibit the enzymes, so a method is needed to determine what enzymes one could use for fluorochrome stained DNA. In this method, DNA is stained with a cyanine dye overnight to allow the dye and DNA to equilibrate. Next, stained DNA is digested with a restriction enzyme, loaded into a gel and electrophoresed. The experimental DNA digest bands are compared to an in silico digest to determine the restriction enzyme activity. If there is the same number of bands as expected, then the reaction is complete. More bands than expected indicate partial digestion and less bands indicate incomplete digestion. The advantage of this method is its simplicity and it uses equipment that a scientist would need for a restriction enzyme assay and gel electrophoresis. A limitation of this method is that the enzymes available to most scientists are commercially available enzymes; however, any restriction enzymes could be used.
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Affiliation(s)
| | - Cody Masters
- Department of Chemistry, University of Nebraska - Kearney
| | | | - Joshua Lallman
- Department of Chemistry, University of Nebraska - Kearney
| | - Drew Thompson
- Department of Chemistry, University of Nebraska - Kearney
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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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Yuan Y, Bayer PE, Batley J, Edwards D. Improvements in Genomic Technologies: Application to Crop Genomics. Trends Biotechnol 2017; 35:547-558. [DOI: 10.1016/j.tibtech.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/13/2022]
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7
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Maschmann A, Kounovsky-Shafer KL. Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:406-417. [PMID: 28362164 DOI: 10.1080/15257770.2017.1300665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.
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Affiliation(s)
- April Maschmann
- a Department of Chemistry , University of Nebraska-Kearney , Kearney , NE , USA
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8
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Abstract
Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex genomes. A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we describe robust and efficient image processing techniques to process these massive datasets and extract accurate restriction maps in the presence of noise, ambiguity and confounding artifacts. We also highlight a few applications of the Optical Mapping system.
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Affiliation(s)
- Prabu Ravindran
- Laboratory of Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, USA
| | - Aditya Gupta
- Laboratory of Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, USA
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9
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Zhou S, Goldstein S, Place M, Bechner M, Patino D, Potamousis K, Ravindran P, Pape L, Rincon G, Hernandez-Ortiz J, Medrano JF, Schwartz DC. A clone-free, single molecule map of the domestic cow (Bos taurus) genome. BMC Genomics 2015; 16:644. [PMID: 26314885 PMCID: PMC4551733 DOI: 10.1186/s12864-015-1823-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 08/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. RESULTS The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts). CONCLUSION Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Michael Place
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Michael Bechner
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Diego Patino
- Departamento de Materiales, Facultad de Minas, Universidad Nacional de Colombia, Sede Medellin, Calle 75 # 79A-51, Bloque M17, Medellin, Colombia, SA.
| | - Konstantinos Potamousis
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Prabu Ravindran
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
| | - Gonzalo Rincon
- Department of Animal Science, University of California-Davis, Davis, CA, 95616, USA.
| | - Juan Hernandez-Ortiz
- Departamento de Materiales, Facultad de Minas, Universidad Nacional de Colombia, Sede Medellin, Calle 75 # 79A-51, Bloque M17, Medellin, Colombia, SA.
| | - Juan F Medrano
- Department of Animal Science, University of California-Davis, Davis, CA, 95616, USA.
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and the UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA.
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Zhu Y, Xu J, Sun C, Zhou S, Xu H, Nelson DR, Qian J, Song J, Luo H, Xiang L, Li Y, Xu Z, Ji A, Wang L, Lu S, Hayward A, Sun W, Li X, Schwartz DC, Wang Y, Chen S. Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense. Sci Rep 2015; 5:11087. [PMID: 26046933 PMCID: PMC4457147 DOI: 10.1038/srep11087] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/14/2015] [Indexed: 11/30/2022] Open
Abstract
Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms.
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Affiliation(s)
- Yingjie Zhu
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Jiang Xu
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Haibin Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jun Qian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Li Xiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Aijia Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Lizhi Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia, 4072
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
| | - Shilin Chen
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
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Cebula TA, Brown EW, Jackson SA, Mammel MK, Mukherjee A, LeClerc JE. Molecular applications for identifying microbial pathogens in the post-9/11 era. Expert Rev Mol Diagn 2014; 5:431-45. [PMID: 15934819 DOI: 10.1586/14737159.5.3.431] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Rapid advances in molecular and optical technologies over the past 10 years have dramatically impacted the way biologic research is conducted today. Examples include microarrays, capillary sequencing, optical mapping and real-time sequencing (Pyrosequencing). These technologies are capable of rapidly delivering massive amounts of genetic information and are becoming routine mainstays of many laboratories. Fortunately, advances in scientific computing have provided the enormous computing power necessary to analyze these enormous data sets. The application of molecular technologies should prove useful to the burgeoning field of microbial forensics. In the post-9/11 era, when securing America's food supply is a major endeavor, the need for rapid identification of microbes that accidentally or intentionally find their way into foods is apparent. The principle that distinguishes a microbial forensic investigation from a molecular epidemiology study is that a biocrime has been committed. If proper attribution is to be attained, a link must be made between a particular microbe in the food and the perpetrator who placed it there. Therefore, the techniques used must be able to discriminate individual isolates of a particular microbe. A battery of techniques in development for distinguishing individual isolates of particular foodborne pathogens is discussed.
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Affiliation(s)
- Thomas A Cebula
- Center for Food Safety & Applied Nutrition, Office of Applied Research & Safety Assessment (HFS-025), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA.
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12
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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13
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Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun 2012; 3:913. [PMID: 22735441 PMCID: PMC3621433 DOI: 10.1038/ncomms1923] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/07/2023] Open
Abstract
Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi. Ganoderma lucidum is a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome of G. lucidum is sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.
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Assessment of whole-genome mapping in a well-defined outbreak of Salmonella enterica serotype Saintpaul. J Clin Microbiol 2012; 50:3063-5. [PMID: 22718933 DOI: 10.1128/jcm.01320-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the use of whole-genome mapping and pulsed-field gel electrophoresis (PFGE) with isolates from an outbreak of Salmonella enterica serotype Saintpaul. PFGE and whole-genome mapping were concordant with 22 of 23 isolates. Whole-genome mapping is a viable alternative tool for the epidemiological analysis of Salmonella food-borne disease investigations.
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15
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Bannantine JP, Wu CW, Hsu C, Zhou S, Schwartz DC, Bayles DO, Paustian ML, Alt DP, Sreevatsan S, Kapur V, Talaat AM. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. BMC Genomics 2012; 13:89. [PMID: 22409516 PMCID: PMC3337245 DOI: 10.1186/1471-2164-13-89] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 03/12/2012] [Indexed: 01/09/2023] Open
Abstract
Background The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map. Results Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the MAP S397 isolate showed it acquired approximately 10 large sequence regions that are shared with the human M. avium subsp. hominissuis strain 104 and lost 2 large regions that are present in the bovine strain. In addition, optical mapping defined the presence of 7 large inversions between the bovine and ovine genomes (~ 2.36 Mb). Whole-genome sequencing of 2 additional sheep strains of MAP (JTC1074 and JTC7565) further confirmed genomic homogeneity of the sheep isolates despite the presence of polymorphisms on the nucleotide level. Conclusions Comparative sequence analysis employed here provided a better understanding of the host association, evolution of members of the M. avium complex and could help in deciphering the phenotypic differences observed among sheep and cattle strains of MAP. A similar approach based on whole-genome sequencing combined with optical mapping could be employed to examine closely related pathogens. We propose an evolutionary scenario for M. avium complex strains based on these genome sequences.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, Iowa, USA.
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Neely RK, Deen J, Hofkens J. Optical mapping of DNA: Single-molecule-based methods for mapping genomes. Biopolymers 2011; 95:298-311. [DOI: 10.1002/bip.21579] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/09/2022]
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Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A 2010; 107:10848-53. [PMID: 20534489 PMCID: PMC2890719 DOI: 10.1073/pnas.0914638107] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Variation in genome structure is an important source of human genetic polymorphism: It affects a large proportion of the genome and has a variety of phenotypic consequences relevant to health and disease. In spite of this, human genome structure variation is incompletely characterized due to a lack of approaches for discovering a broad range of structural variants in a global, comprehensive fashion. We addressed this gap with Optical Mapping, a high-throughput, high-resolution single-molecule system for studying genome structure. We used Optical Mapping to create genome-wide restriction maps of a complete hydatidiform mole and three lymphoblast-derived cell lines, and we validated the approach by demonstrating a strong concordance with existing methods. We also describe thousands of new variants with sizes ranging from kb to Mb.
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Affiliation(s)
- Brian Teague
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Michael S. Waterman
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Steven Goldstein
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Konstantinos Potamousis
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Shiguo Zhou
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Susan Reslewic
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Deepayan Sarkar
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
| | - Anton Valouev
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Christopher Churas
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Jeffrey M. Kidd
- Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195-5065
| | - Scott Kohn
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Rodney Runnheim
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Casey Lamers
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Dan Forrest
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
- Department of Biostatistics and Medical Informatics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195-5065
| | - Marijo Kent-First
- Department of Animal Science, Department of Biological Sciences, Mississippi State University, 130 Harned Hall, Lee Boulevard, Mississippi State, MS 39762-9698
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213-2536; and
| | - Miron Livny
- Department of Computer Sciences, University of Wisconsin, 1210 West Dayton Street, Madison, WI 53706-1685
| | - David C. Schwartz
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
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Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet 2009; 5:e1000711. [PMID: 19936062 PMCID: PMC2774507 DOI: 10.1371/journal.pgen.1000711] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. The maize genome contains abundant repeats interspersed by low-copy, gene-coding sequences that make it a challenge to sequence; consequently, current BAC sequence assemblies average 11 contigs per clone. The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps, but the B73 genome structure could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide, high-resolution optical map of maize B73 genome that was constructed from the direct analysis of genomic DNA molecules without using genetic markers. The integration of optical and iMap resources with comparisons to FPC maps enabled a uniquely comprehensive and scalable assessment of a given BAC's sequence assembly, its placement within a FPC contig, and the location of this FPC contig within a chromosome-wide pseudomolecule. As such, the overall utility of the maize optical map for the validation of sequence assemblies has been significant and demonstrates the inherent advantages of single molecule platforms. Construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Fusheng Wei
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - John Nguyen
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Mike Bechner
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Konstantinos Potamousis
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael R. Mehan
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Chris Churas
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dan K. Forrest
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Roger Wise
- Corn Insects and Crop Genetics Research, United States Department of Agriculture–Agricultural Research Service and Department of Plant Pathology, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Plant, Soil, and Nutrition Research, United States Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Rod A. Wing
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Michael S. Waterman
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Miron Livny
- Computer Sciences Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Hernández-Ortiz JP, Chopra M, Geier S, de Pablo JJ. Hydrodynamic effects on the translocation rate of a polymer through a pore. J Chem Phys 2009; 131:044904. [DOI: 10.1063/1.3184798] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Wu CW, Schramm TM, Zhou S, Schwartz DC, Talaat AM. Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome. BMC Genomics 2009; 10:25. [PMID: 19146697 PMCID: PMC2633350 DOI: 10.1186/1471-2164-10-25] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 01/15/2009] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Infection of cattle with Mycobacterium avium subspecies paratuberculosis (M. ap) causes severe economic losses to the dairy industry in the USA and worldwide. In an effort to better examine diversity among M. ap strains, we used optical mapping to profile genomic variations between strains of M. ap K-10 (sequenced strain) and M. ap ATCC 19698 (type strain). RESULTS The assembled physical restriction map of M. ap ATCC 19698 showed a genome size of 4,839 kb compared to the sequenced K-10 genome of 4,830 kb. Interestingly, alignment of the optical map of the M. ap ATCC 19698 genome to the complete M. ap K-10 genome sequence revealed a 648-kb inversion around the origin of replication. However, Southern blotting, PCR amplification and sequencing analyses of the inverted region revealed that the genome of M. ap K-10 differs from the published sequence in the region starting from 4,197,080 bp to 11,150 bp, spanning the origin of replication. Additionally, two new copies of the coding sequences > 99.8% were identified, identical to the MAP0849c and MAP0850c genes located immediately downstream of the MAP3758c gene. CONCLUSION The optical map of M. ap ATCC 19698 clearly indicated the miss-assembly of the sequenced genome of M. ap K-10. Moreover, it identified 2 new genes in M. ap K-10 genome. This analysis strongly advocates for the utility of physical mapping protocols to complement genome sequencing projects.
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Affiliation(s)
- Chia-wei Wu
- The Laboratory of Bacterial Genomics, Department of Pathobiological Sciences, University of Wisconsin-Madison, WI, USA.
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21
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Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, Churas CP, Bergendahl V, Thomson JA, Schwartz DC. Optical mapping discerns genome wide DNA methylation profiles. BMC Mol Biol 2008; 9:68. [PMID: 18667073 PMCID: PMC2516518 DOI: 10.1186/1471-2199-9-68] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 07/30/2008] [Indexed: 11/23/2022] Open
Abstract
Background Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification. Results A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping. Conclusion The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies.
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Affiliation(s)
- Gene E Ananiev
- Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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22
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Zhou S, Bechner MC, Place M, Churas CP, Pape L, Leong SA, Runnheim R, Forrest DK, Goldstein S, Livny M, Schwartz DC. Validation of rice genome sequence by optical mapping. BMC Genomics 2007; 8:278. [PMID: 17697381 PMCID: PMC2048515 DOI: 10.1186/1471-2164-8-278] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 08/15/2007] [Indexed: 11/30/2022] Open
Abstract
Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences revealed by optical maps constructed from a broad range of rice subspecies and varieties.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael C Bechner
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael Place
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Chris P Churas
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sally A Leong
- USDA-ARS, CCRU, Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rod Runnheim
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dan K Forrest
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Miron Livny
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
- Department of Chemistry, Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics; University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One 2007; 2:e484. [PMID: 17534434 PMCID: PMC1871613 DOI: 10.1371/journal.pone.0000484] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 05/05/2007] [Indexed: 11/18/2022] Open
Abstract
While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHort Read Assembly Protocol), a sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. We describe a variation on hierarchical sequencing with two crucial differences: (1) we select a clone library from the genome randomly rather than as a tiling path and (2) we sample clones from the genome at high coverage and reads from the clones at low coverage. We assume that 200 bp read lengths with a 1% error rate and inexpensive random fragment cloning on whole mammalian genomes is feasible. Our assembly methodology is based on first ordering the clones and subsequently performing read assembly in three stages: (1) local assemblies of regions significantly smaller than a clone size, (2) clone-sized assemblies of the results of stage 1, and (3) chromosome-sized assemblies. By aggressively localizing the assembly problem during the first stage, our method succeeds in assembling short, unpaired reads sampled from repetitive genomes. We tested our assembler using simulated reads from D. melanogaster and human chromosomes 1, 11, and 21, and produced assemblies with large sets of contiguous sequence and a misassembly rate comparable to other draft assemblies. Tested on D. melanogaster and the entire human genome, our clone-ordering method produces accurate maps, thereby localizing fragment assembly and enabling the parallelization of the subsequent steps of our pipeline. Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian genomes will soon be possible with high-throughput, short-read technologies using our methodology.
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Affiliation(s)
- Andreas Sundquist
- Department of Computer Science, Stanford University, Stanford, California, United States of America.
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24
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Hernández-Ortiz JP, de Pablo JJ, Graham MD. Fast computation of many-particle hydrodynamic and electrostatic interactions in a confined geometry. PHYSICAL REVIEW LETTERS 2007; 98:140602. [PMID: 17501260 DOI: 10.1103/physrevlett.98.140602] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Indexed: 05/15/2023]
Abstract
An O(N) method is presented for calculation of hydrodynamic or electrostatic interactions between N point particles in a confined geometry. This approach splits point forces or sources into a local contribution for which rapidly decaying free-space analytical solutions to the Stokes or Poisson equations are used, and a global contribution whose effect is determined numerically using a fast iterative method. The scheme is applied to Brownian dynamics simulations of flowing confined polymer solutions, and the effects of concentration on hydrodynamically induced migration phenomena are illustrated.
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Affiliation(s)
- Juan P Hernández-Ortiz
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
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25
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Choudhary M, Zanhua X, Fu YX, Kaplan S. Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II. J Bacteriol 2006; 189:1914-21. [PMID: 17172323 PMCID: PMC1855717 DOI: 10.1128/jb.01498-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three strains of Rhodobacter sphaeroides of diverse origin have been under investigation in our laboratory for their genome complexities, including the presence of multiple chromosomes and the distribution of essential genes within their genomes. The genome of R. sphaeroides 2.4.1 has been completely sequenced and fully annotated, and now two additional strains (ATCC 17019 and ATCC 17025) of R. sphaeroides have been sequenced. Thus, genome comparisons have become a useful approach in determining the evolutionary relationships among different strains of R. sphaeroides. In this study, the concatenated chromosomal sequences from the three strains of R. sphaeroides were aligned, using Mauve, to examine the extent of shared DNA regions and the degree of relatedness among their chromosome-specific DNA sequences. In addition, the exact intra- and interchromosomal DNA duplications were analyzed using Mummer. Genome analyses employing these two independent approaches revealed that strain ATCC 17025 diverged considerably from the other two strains, 2.4.1 and ATCC 17029, and that the two latter strains are more closely related to one another. Results further demonstrated that chromosome II (CII)-specific DNA sequences of R. sphaeroides have rapidly evolved, while CI-specific DNA sequences have remained highly conserved. Aside from the size variation of CII of R. sphaeroides, variation in sequence lengths of the CII-shared DNA regions and their high sequence divergence among strains of R. sphaeroides suggest the involvement of CII in the evolution of strain-specific genomic rearrangements, perhaps requiring strains to adapt in specialized niches.
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Affiliation(s)
- M Choudhary
- Department of Microbiology and Molecular Genetics, The University of Texas Medical School, Houston, Texas 77030, USA
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26
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Wu T, Schwartz DC. Transchip: single-molecule detection of transcriptional elongation complexes. Anal Biochem 2006; 361:31-46. [PMID: 17187751 PMCID: PMC1945215 DOI: 10.1016/j.ab.2006.10.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 10/30/2006] [Accepted: 10/30/2006] [Indexed: 11/24/2022]
Abstract
A new single-molecule system, Transchip, was developed for analysis of transcription products at their genomic origins. The bacteriophage T7 RNA polymerase and its promoters were used in a model system, and resultant RNAs were imaged and detected at their positions along single template DNA molecules. The Transchip system has drawn from critical aspects of Optical Mapping, a single-molecule system that enables the construction of high-resolution ordered restriction maps of whole genomes from single DNA molecules. Through statistical analysis of hundreds of single-molecule template/transcript complexes, Transchip enables analysis of the locations and strength of promoters, the direction and processivity of transcription reactions, and the termination of transcription. These novel results suggest that the new system may serve as a high-throughput platform to investigate transcriptional events on a large genome-wide scale.
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Affiliation(s)
- Tian Wu
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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27
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Valouev A, Schwartz DC, Zhou S, Waterman MS. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A 2006; 103:15770-5. [PMID: 17043225 PMCID: PMC1635078 DOI: 10.1073/pnas.0604040103] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Indexed: 11/18/2022] Open
Abstract
The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are "in the noise" or "slightly above the noise." We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.
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Affiliation(s)
- Anton Valouev
- Department of Mathematics, University of Southern California, 3620 South Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA.
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Tavano CL, Donohue TJ. Development of the bacterial photosynthetic apparatus. Curr Opin Microbiol 2006; 9:625-31. [PMID: 17055774 PMCID: PMC2765710 DOI: 10.1016/j.mib.2006.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 10/11/2006] [Indexed: 11/29/2022]
Abstract
Anoxygenic photosynthetic bacteria have provided us with crucial insights into the process of solar energy capture, pathways of metabolic and societal importance, specialized differentiation of membrane domains, function or assembly of bioenergetic enzymes, and into the genetic control of these and other activities. Recent insights into the organization of this bioenergetic membrane system, the genetic control of this specialized domain of the inner membrane and the process by which potentially photosynthetic and non-photosynthetic cells protect themselves from an important class of reactive oxygen species will provide an unparalleled understanding of solar energy capture and facilitate the design of solar-powered microbial biorefineries.
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Affiliation(s)
- Christine L Tavano
- Bacteriology Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, de Pablo JJ, Graham MD, Coppersmith SN, Goldstein S, Schwartz DC. A microfluidic system for large DNA molecule arrays. Anal Chem 2006; 76:5293-301. [PMID: 15362885 DOI: 10.1021/ac0496401] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single molecule approaches offer the promise of large, exquisitely miniature ensembles for the generation of equally large data sets. Although microfluidic devices have previously been designed to manipulate single DNA molecules, many of the functionalities they embody are not applicable to very large DNA molecules, normally extracted from cells. Importantly, such microfluidic devices must work within an integrated system to enable high-throughput biological or biochemical analysis-a key measure of any device aimed at the chemical/biological interface and required if large data sets are to be created for subsequent analysis. The challenge here was to design an integrated microfluidic device to control the deposition or elongation of large DNA molecules (up to millimeters in length), which would serve as a general platform for biological/biochemical analysis to function within an integrated system that included massively parallel data collection and analysis. The approach we took was to use replica molding to construct silastic devices to consistently deposit oriented, elongated DNA molecules onto charged surfaces, creating massive single molecule arrays, which we analyzed for both physical and biochemical insights within an integrated environment that created large data sets. The overall efficacy of this approach was demonstrated by the restriction enzyme mapping and identification of single human genomic DNA molecules.
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Affiliation(s)
- Eileen T Dimalanta
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, Wisconsin 53706, USA
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30
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Chai Y, Winans SC. RepB protein of an Agrobacterium tumefaciens Ti plasmid binds to two adjacent sites between repA and repB for plasmid partitioning and autorepression. Mol Microbiol 2006; 58:1114-29. [PMID: 16262794 DOI: 10.1111/j.1365-2958.2005.04886.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmids of Agrobacterium tumefaciens replicate using the products of the repABC operon, which are highly conserved among plasmids and some chromosomes of the alpha-Proteobacteria. The products of repA and repB direct plasmid partitioning, while the repC gene encodes a replication initiator protein. The transcription of the repABC operon of tumour inducing (Ti) plasmids is both negatively autoregulated by the RepA and RepB proteins, and positively regulated by TraR. In the present study, we have identified a fourth gene (repD) in the repABC operon of an octopine-type Ti plasmid. repD is 78 codons in length, and maps between repA and repB genes. A repD-lacZ protein fusion demonstrated that repD is strongly expressed. Two identical binding sites for the RepB protein were found within the repD coding sequence, and these sites are required for plasmid stability and for maximal repression of repABC transcription. RepA protein enhances the binding of RepB at these binding sites, just as RepB increases the affinity of RepA for binding sites at the repABC P4 promoter. We propose that RepA and RepB form complexes that bind both sites, possibly causing a loop that is important for repression of the repABC operon. Binding at one or both sites may also be required for accurate plasmid partitioning.
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Affiliation(s)
- Yunrong Chai
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
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31
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Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Lafton A, Latgé JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peñalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Córdoba S, Rodríguez-Peña JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 2006; 438:1151-6. [PMID: 16372009 DOI: 10.1038/nature04332] [Citation(s) in RCA: 989] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 10/12/2005] [Indexed: 11/09/2022]
Abstract
Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.
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32
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Reslewic S, Zhou S, Place M, Zhang Y, Briska A, Goldstein S, Churas C, Runnheim R, Forrest D, Lim A, Lapidus A, Han CS, Roberts GP, Schwartz DC. Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl Environ Microbiol 2005; 71:5511-22. [PMID: 16151144 PMCID: PMC1214604 DOI: 10.1128/aem.71.9.5511-5522.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2005] [Accepted: 04/11/2005] [Indexed: 11/20/2022] Open
Abstract
Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a "molecular cytogenetics" approach to solving problems in genomic analysis.
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Affiliation(s)
- Susan Reslewic
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
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33
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Abstract
The prevalence of the two-chromosome configuration was investigated in 34 species of vibrios and closely related species. Pulsed-field gel electrophoresis of undigested genomic DNA suggested that vibrios commonly have two chromosomes. The size of the large chromosome is predominantly within a narrow range (3.0 to 3.3 Mb), whereas the size of the small chromosome varies considerably among the vibrios (0.8 to 2.4 Mb). This fact suggests that the structure of the small chromosome is more flexible than that of the large chromosome during the evolution of vibrios.
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Affiliation(s)
- Kazuhisa Okada
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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34
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Ferris MM, Yoshida TM, Marrone BL, Keller RA. Fingerprinting of single viral genomes. Anal Biochem 2005; 337:278-88. [PMID: 15691508 DOI: 10.1016/j.ab.2004.10.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Indexed: 11/30/2022]
Abstract
We demonstrate the use of technology developed for optical mapping to acquire DNA fingerprints from single genomes for the purpose of discrimination and identification of bacteria and viruses. Single genome fingerprinting (SGF) provides not only the size but also the order of the restriction fragments, which adds another dimension to the information that can be used for discrimination. Analysis of single organisms may eliminate the need to culture cells and thereby significantly reduce analysis time. In addition, samples containing mixtures of several organisms can be analyzed. For analysis, cells are embedded in an agarose matrix, lysed, and processed to yield intact DNA. The DNA is then deposited on a derivatized glass substrate. The elongated genome is digested with a restriction enzyme and stained with the intercalating dye YOYO-1. DNA is then quantitatively imaged with a fluorescence microscope and the fragments are sized to an accuracy >or=90% by their fluorescence intensity and contour length. Single genome fingerprints were obtained from pure samples of adenovirus, from bacteriophages lambda and T4 GT7, and from a mixture of the three viral genomes. SGF will enable the fingerprinting of uncultured and unamplified samples and allow rapid identification of microorganisms with applications in forensics, medicine, public health, and environmental microbiology.
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Affiliation(s)
- Matthew M Ferris
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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35
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Min H, Guo H, Xiong J. Rhythmic gene expression in a purple photosynthetic bacterium,Rhodobacter sphaeroides. FEBS Lett 2005; 579:808-12. [PMID: 15670851 DOI: 10.1016/j.febslet.2005.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 01/03/2005] [Accepted: 01/04/2005] [Indexed: 11/16/2022]
Abstract
Circadian rhythms are known to exist in all groups of eukaryotic organisms as well as oxygenic photosynthetic bacteria, cyanobacteria. However, little information is available regarding the existence of rhythmic behaviors in prokaryotes other than cyanobacteria. Here we report biological rhythms of gene expression in a purple bacterium Rhodobacter sphaeroides by using a luciferase reporter gene system. Self-bioluminescent strains of Rb. sphaeroides were constructed, which produced a bacterial luciferase and its substrate, a long chain fatty aldehyde, to sustain the luminescence reaction. After being subjected to a temperature or light entrainment regime, the reporter strains with the luciferase genes driven by an upstream endogenous promoter expressed self-sustained rhythmicity in the constant free-running period. The rhythms were controlled by oxygen and exhibited a circadian period of 20.5 h under aerobic conditions and an ultradian period of 10.6-12.7 h under anaerobic conditions. The data suggest a novel endogenous oscillation mechanism in purple photosynthetic bacteria. Elucidation of the clock-like behavior in purple bacteria has implications in understanding the origin and evolution of circadian rhythms.
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Affiliation(s)
- Hongtao Min
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
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36
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Nierman WC, May G, Kim HS, Anderson MJ, Chen D, Denning DW. What theAspergillusgenomes have told us. Med Mycol 2005; 43 Suppl 1:S3-5. [PMID: 16110785 DOI: 10.1080/13693780400029049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The sequencing and annotation of the genomes of the first strains of Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus will be seen in retrospect as a transformational event in Aspergillus biology. With this event the entire genetic composition of A. nidulans, the sexual experimental model organism of the genus Aspergillus, A. oryzae, the food biotechnology organism which is the product of centuries of cultivation, and A. fumigatus, the most common causative agent of invasive aspergillosis is now revealed to the extent that we are at present able to understand. Each genome exhibits a large set of genes common to the three as well as a much smaller set of genes unique to each. Moreover, these sequences serve as resources providing the major tool to expanding our understanding of the biology of each. Transcription profiling of A. fumigatus at high temperatures and comparative genomic hybridization between A. fumigatus and a closely related Aspergillus species provides microarray based examples of the beginning of functional analysis of the genomes of these organisms going forward from the genome sequence.
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Affiliation(s)
- W C Nierman
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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37
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Zhou S, Kile A, Bechner M, Place M, Kvikstad E, Deng W, Wei J, Severin J, Runnheim R, Churas C, Forrest D, Dimalanta ET, Lamers C, Burland V, Blattner FR, Schwartz DC. Single-molecule approach to bacterial genomic comparisons via optical mapping. J Bacteriol 2004; 186:7773-82. [PMID: 15516592 PMCID: PMC524920 DOI: 10.1128/jb.186.22.7773-7782.2004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computation Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
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38
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Zhou S, Kile A, Kvikstad E, Bechner M, Severin J, Forrest D, Runnheim R, Churas C, Anantharaman TS, Myler P, Vogt C, Ivens A, Stuart K, Schwartz DC. Shotgun optical mapping of the entire Leishmania major Friedlin genome. Mol Biochem Parasitol 2004; 138:97-106. [PMID: 15500921 DOI: 10.1016/j.molbiopara.2004.08.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 08/02/2004] [Indexed: 11/21/2022]
Abstract
Leishmania is a group of protozoan parasites which causes a broad spectrum of diseases resulting in widespread human suffering and death, as well as economic loss from the infection of some domestic animals and wildlife. To further understand the fundamental genomic architecture of this parasite, and to accelerate the on-going sequencing project, a whole-genome XbaI restriction map was constructed using the optical mapping system. This map supplemented traditional physical maps that were generated by fingerprinting and hybridization of cosmid and P1 clone libraries. Thirty-six optical map contigs were constructed for the corresponding known 36 chromosomes of the Leishmania major Friedlin genome. The chromosome sizes ranged from 326.9 to 2821.3 kb, with a total genome size of 34.7 Mb; the average XbaI restriction fragment was 25.3 kb, and ranged from 15.7 to 77.8 kb on a per chromosomes basis. Comparison between the optical maps and the in silico maps of sequence drawn from completed, nearly finished, or large sequence contigs showed that optical maps served several useful functions within the path to create finished sequence by: guiding aspects of the sequence assembly, identifying misassemblies, detection of cosmid or PAC clones misplacements to chromosomes, and validation of sequence stemming from varying degrees of finishing. Our results also showed the potential use of optical maps as a means to detect and characterize map segmental duplication within genomes.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
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