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Gu X, Ye T, Zhang XR, Nie L, Wang H, Li W, Lu R, Fu C, Du LL, Zhou JQ. Single-chromosome fission yeast models reveal the configuration robustness of a functional genome. Cell Rep 2022; 40:111237. [PMID: 36001961 DOI: 10.1016/j.celrep.2022.111237] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 07/28/2022] [Indexed: 11/03/2022] Open
Abstract
In eukaryotic organisms, genetic information is usually carried on multiple chromosomes. Whether and how the number and configuration of chromosomes affect organismal fitness and speciation remain unclear. Here, we have successfully established several single-chromosome fission yeast Schizosaccharomyces pombe strains, in which the three natural chromosomes have been fused into one giant chromosome in different orders. Chromosome fusions accompanied by the deletions of telomeres and centromeres result in the loss of chromosomal interactions and a drastic change of global chromosome organization, but alter gene expression marginally. The single-chromosome strains display little defects in cell morphology, mitosis, genotoxin sensitivity, and meiosis. Crosses between a wild-type strain and a single-chromosome strain or between two single-chromosome strains with different fusion orders suffer defective meiosis and poor spore viability. We conclude that eukaryotic genomes are robust against dramatic chromosomal reconfiguration, and stochastic changes in chromosome number and genome organization during evolution underlie reproductive isolation and speciation.
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Affiliation(s)
- Xin Gu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Ye
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lingyun Nie
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huan Wang
- Frasergen Bioinformatics, Wuhan, China
| | - Wei Li
- Frasergen Bioinformatics, Wuhan, China
| | - Rui Lu
- Frasergen Bioinformatics, Wuhan, China
| | - Chuanhai Fu
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, CAS Center for Excellence in Molecular Cell Sciences, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Jin-Qiu Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou 310024, China.
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de Carvalho JA, Monteiro RC, Hagen F, de Camargo ZP, Rodrigues AM. Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species. J Fungi (Basel) 2022; 8:jof8080809. [PMID: 36012797 PMCID: PMC9409836 DOI: 10.3390/jof8080809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.
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Affiliation(s)
- Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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Ayukawa Y, Taga M. Karyotyping of Fusarium oxysporum by Pulsed-Field Gel Electrophoresis and the Germ Tube Burst Method. Methods Mol Biol 2022; 2391:31-43. [PMID: 34686974 DOI: 10.1007/978-1-0716-1795-3_3] [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] [Indexed: 06/13/2023]
Abstract
In fungi, karyotyping is fundamental to understanding their genome organization. It is also essential to study various genome- or chromosome-related topics such as karyotype polymorphisms and supernumerary or pathogenicity chromosomes. Here, we describe the protocols of pulsed-field gel electrophoresis and the germ tube burst method for molecular and cytological karyotyping of Fusarium oxysporum. The combined use of the two methods is valuable for determining definitive and comprehensive karyotypes of these fungi.
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Affiliation(s)
- Yu Ayukawa
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Masatoki Taga
- Department of Biology, Faculty of Science, Okayama University, Okayama, Japan.
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Plaumann PL, Schmidpeter J, Dahl M, Taher L, Koch C. A Dispensable Chromosome Is Required for Virulence in the Hemibiotrophic Plant Pathogen Colletotrichum higginsianum. Front Microbiol 2018; 9:1005. [PMID: 29867895 PMCID: PMC5968395 DOI: 10.3389/fmicb.2018.01005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/30/2018] [Indexed: 01/01/2023] Open
Abstract
The hemibiotrophic plant pathogen Colletotrichum higginsianum infects Brassicaceae and in combination with Arabidopsis thaliana, represents an important model system to investigate various ecologically important fungal pathogens and their infection strategies. After penetration of plant cells by appressoria, C. higginsianum establishes large biotrophic primary hyphae in the first infected cell. Shortly thereafter, a switch to necrotrophic growth occurs leading to the invasion of neighboring cells by secondary hyphae. In a forward genetic screen for virulence mutants by insertional mutagenesis, we identified mutants that penetrate the plant but show a defect in the passage from biotrophy to necrotrophy. Genome sequencing and pulsed-field gel electrophoresis revealed that two mutants were lacking chromosome 11, encoding potential pathogenicity genes. We established a chromosome loss assay to verify that strains lacking this small chromosome abort infection during biotrophy, while their ability to grow on artificial media was not affected. C. higginsianum harbors a second small chromosome, which can be lost without effects on virulence or growth on agar plates. Furthermore, we found that chromosome 11 is required to suppress Arabidopsis thaliana plant defense mechanisms dependent on tryptophan derived secondary metabolites.
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Affiliation(s)
- Peter-Louis Plaumann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schmidpeter
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marlis Dahl
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leila Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Koch
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Mehrabi R, Mirzadi Gohari A, Kema GHJ. Karyotype Variability in Plant-Pathogenic Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:483-503. [PMID: 28777924 DOI: 10.1146/annurev-phyto-080615-095928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent advances in genetic and molecular technologies gradually paved the way for the transition from traditional fungal karyotyping to more comprehensive chromosome biology studies. Extensive chromosomal polymorphisms largely resulting from chromosomal rearrangements (CRs) are widely documented in fungal genomes. These extraordinary CRs in fungi generate substantial genome plasticity compared to other eukaryotic organisms. Here, we review the most recent findings on fungal CRs and their underlying mechanisms and discuss the functional consequences of CRs for adaptation, fungal evolution, host range, and pathogenicity of fungal plant pathogens in the context of chromosome biology. In addition to a complement of permanent chromosomes called core chromosomes, the genomes of many fungal pathogens comprise distinct unstable chromosomes called dispensable chromosomes (DCs) that also contribute to chromosome polymorphisms. Compared to the core chromosomes, the structural features of DCs usually differ for gene density, GC content, housekeeping genes, and recombination frequency. Despite their dispensability for normal growth and development, DCs have important biological roles with respect to pathogenicity in some fungi but not in others. Therefore, their evolutionary origin is also reviewed in relation to overall fungal physiology and pathogenicity.
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Affiliation(s)
- Rahim Mehrabi
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
| | - Gert H J Kema
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
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6
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Tazawa S, Kobayashi K, Oyoshi T, Yamanaka M. Supramolecular gel electrophoresis of large DNA fragments. Electrophoresis 2017; 38:2662-2665. [PMID: 28681974 DOI: 10.1002/elps.201700223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 11/10/2022]
Abstract
Pulsed-field gel electrophoresis is a frequent technique used to separate exceptionally large DNA fragments. In a typical continuous field electrophoresis, it is challenging to separate DNA fragments larger than 20 kbp because they migrate at a comparable rate. To overcome this challenge, it is necessary to develop a novel matrix for the electrophoresis. Here, we describe the electrophoresis of large DNA fragments up to 166 kbp using a supramolecular gel matrix and a typical continuous field electrophoresis system. C3 -symmetric tris-urea self-assembled into a supramolecular hydrogel in tris-boric acid-EDTA buffer, a typical buffer for DNA electrophoresis, and the supramolecular hydrogel was used as a matrix for electrophoresis to separate large DNA fragments. Three types of DNA marker, the λ-Hind III digest (2 to 23 kbp), Lambda DNA-Mono Cut Mix (10 to 49 kbp), and Marker 7 GT (10 to 165 kbp), were analyzed in this study. Large DNA fragments of greater than 100 kbp showed distinct mobility using a typical continuous field electrophoresis system.
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Affiliation(s)
- Shohei Tazawa
- Department of Chemistry, Shizuoka University, Shizuoka, Japan
| | | | - Takanori Oyoshi
- Department of Chemistry, Shizuoka University, Shizuoka, Japan
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7
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Mehrabi R, Taga M, Kema GH. Electrophoretic and cytological karyotyping of the foliar wheat pathogenMycosphaerella graminicolareveals many chromosomes with a large size range. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rahim Mehrabi
- Wageningen University and Research Centre, Plant Research International B.V., P.O. Box 16, 6700 AA, Wageningen, the Netherlands
| | - Masatoki Taga
- Department of Biology, Faculty of Science, Okayama University, Tsushima-naka, Okayama 700-8530, Japan
| | - Gert H.J. Kema
- Plant Research International B.V., P.O. Box 16, 6700 AA, Wageningen, the Netherlands
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Structural organization of very small chromosomes: study on a single-celled evolutionary distant eukaryote Giardia intestinalis. Chromosoma 2014; 124:81-94. [DOI: 10.1007/s00412-014-0486-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022]
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9
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Akamatsu HO, Chilvers MI, Kaiser WJ, Peever TL. Karyotype polymorphism and chromosomal rearrangement in populations of the phytopathogenic fungus, Ascochyta rabiei. Fungal Biol 2012; 116:1119-33. [PMID: 23153803 DOI: 10.1016/j.funbio.2012.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/02/2012] [Indexed: 01/12/2023]
Abstract
The fungus Ascochyta rabiei is the causal agent of Ascochyta blight of chickpea and the most serious threat to chickpea production. Little is currently known about the genome size or organization of A. rabiei. Given recent genome sequencing efforts, characterization of the genome at a population scale will provide a framework for genome interpretation and direction of future resequencing efforts. Electrophoretic karyotype profiles of 112 isolates from 21 countries revealed 12-16 chromosomes between 0.9 Mb and 4.6 Mb with an estimated genome size of 23 Mb-34 Mb. Three general karyotype profiles A, B, and C were defined by the arrangement of the largest chromosomes. Approximately one-third of isolates (group A) possessed a chromosome larger than 4.0 Mb that was absent from group B and C isolates. The ribosomal RNA gene (rDNA) cluster was assigned to the largest chromosome in all except four isolates (group C) whose rDNA cluster was located on the second largest chromosome (3.2 Mb). Analysis of progeny from an in vitro sexual cross between two group B isolates revealed one of 16 progeny with an rDNA-encoding chromosome larger than 4.0 Mb similar to group A isolates, even though a chromosome of this size was not present in either parent. No expansion of the rDNA cluster was detected in the progeny, indicating the increase in chromosome size was not due to an expansion in number of rDNA repeats. The karyotype of A. rabiei is relatively conserved when compared with published examples of asexual ascomycetes, but labile with the potential for large scale chromosomal rearrangements during meiosis. The results of this study will allow for the targeted sequencing of specific isolates to determine the molecular mechanisms of karyotype variation within this species.
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Affiliation(s)
- Hajime O Akamatsu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
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Fu R, Ding L, Zhu J, Li P, Zheng AP. Morphological structure of propagules and electrophoretic karyotype analysis of false smut Villosiclava virens in rice. J Microbiol 2012; 50:263-9. [DOI: 10.1007/s12275-012-1456-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/08/2011] [Indexed: 11/30/2022]
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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Nichols NN, Szynkarek MP, Skory CD, Gorsich SW, López MJ, Guisado GM, Nichols WA. Transformation and electrophoretic karyotyping of Coniochaeta ligniaria NRRL30616. Curr Genet 2011; 57:169-75. [DOI: 10.1007/s00294-010-0332-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 12/22/2010] [Accepted: 12/24/2010] [Indexed: 10/18/2022]
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Dujardin JC. Structure, dynamics and function of Leishmania genome: Resolving the puzzle of infection, genetics and evolution? INFECTION GENETICS AND EVOLUTION 2009; 9:290-7. [DOI: 10.1016/j.meegid.2008.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 11/25/2008] [Accepted: 11/25/2008] [Indexed: 01/23/2023]
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Eusebio-Cope A, Suzuki N, Sadeghi-Garmaroodi H, Taga M. Cytological and electrophoretic karyotyping of the chestnut blight fungus Cryphonectria parasitica. Fungal Genet Biol 2009; 46:342-51. [PMID: 19570503 DOI: 10.1016/j.fgb.2009.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
Abstract
The karyotypes of nine strains including three transformants of the chestnut blight fungus Cryphonectria parasitica were analyzed by pulsed-field gel electrophoresis (PFGE) and cytology using a fluorescence microscope. Cytology of the mitotic metaphase showed n=9 for both standard strain EP155 and field strain GH2 infected by Cryphonectria hypovirus 3. Chromosomes were morphologically characterized by size, heterochromatic segment, and constriction. PFGE resolved 5 or 6 chromosomal DNA bands ranging from 3.3Mbp to 9.7Mbp, but accurate determination of the chromosome number was hampered by clumping of some bands. Banding profiles in PFGE were similar among the strains except for GH2, in which a chromosome translocation was detected by Southern blot analysis. By integrating the data from cytology and PFGE, the genome size of C. parasitica was estimated to be ca. 50Mbp. This is the first report of a cytological karyotype in the order Diaporthales.
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Affiliation(s)
- Ana Eusebio-Cope
- Agrivirology Laboratory, Research Institute for Bioresources, Okayama University, Kurashiki, Japan
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15
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Manzo-Sánchez G, Zapater MF, Luna-Martínez F, Conde-Ferráez L, Carlier J, James-Kay A, Simpson J. Construction of a genetic linkage map of the fungal pathogen of banana Mycosphaerella fijiensis, causal agent of black leaf streak disease. Curr Genet 2008; 53:299-311. [PMID: 18365202 DOI: 10.1007/s00294-008-0186-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 12/15/2022]
Abstract
A genetic linkage map of the fungal plant pathogen Mycosphaerella fijiensis, causal agent of black leaf streak disease of banana was developed. A cross between the isolates CIRAD86 (from Cameroon) and CIRAD139A (from Colombia) was analyzed using molecular markers and the MAT locus. The genetic linkage map consists of 298 AFLP and 16 SSR markers with 23 linkage groups, containing five or more markers, covering 1,879 cM. Markers are separated on average by around 5.9 cM. The MAT locus was shown to segregate in a 1:1 ratio but could not be successfully mapped. An estimate of the relation between physical size and genetic distance was approximately 39.0 kb/cM. The estimated total haploid genome size was calculated using the genetic mapping data at 4,298.2 cM. This is the first genetic linkage map reported for this important foliar pathogen of banana. The great utility of the map will be for anchoring contigs in the genome sequence, evolutionary studies in comparison with other fungi, to identify quantitative trait loci (QTLs) associated with aggressiveness or oxidative stress resistance and with the recently available genome sequence, for positional cloning.
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Affiliation(s)
- Gilberto Manzo-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130. Colonia Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
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Aggio FB, Farah ME, de Melo GB, d'Azevedo PA, Pignatari ACC, Höfling-Lima AL. Acute endophthalmitis following intravitreal bevacizumab (Avastin) injection. Eye (Lond) 2007; 21:408-9. [PMID: 17277758 DOI: 10.1038/sj.eye.6702683] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To report two cases of acute endophthalmitis following intravitreal bevacizumab injection. METHODS Two patients with exudative age-related macular degeneration were treated sequentially with an intravitreal injection of bevacizumab and developed signs of severe but painless infectious endophthalmitis 2 days later. Vitreous samples were obtained, followed by the injection of vancomycin 1 mg/0.1 ml and ceftazidime 2.25 mg/0.1 ml. Pulsed-field gel electrophoresis (PFGE) was used to determine whether the isolated microorganisms were the same. RESULTS Coagulase-negative staphylococci were identified and isolated from the vitreous specimen of both patients. PFGE revealed different patterns of banding, excluding that interpatient contamination occured. CONCLUSIONS Infectious endophthalmitis is a potential complication of intravitreal bevacizumab injection.
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Affiliation(s)
- F B Aggio
- Vision Institute, Federal University of São Paulo, São Paulo, Brazil
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Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD. Eukaryotic genome size databases. Nucleic Acids Res 2007; 35:D332-8. [PMID: 17090588 PMCID: PMC1669731 DOI: 10.1093/nar/gkl828] [Citation(s) in RCA: 268] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 10/04/2006] [Indexed: 12/02/2022] Open
Abstract
Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (www.kew.org/genomesize/homepage.html), the Animal Genome Size Database (www.genomesize.com) and the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/). In total, these databases provide freely accessible genome size data for >10,000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs.
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Affiliation(s)
- T Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, Brisse S, Struelens M. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect 2007; 13 Suppl 3:1-46. [PMID: 17716294 DOI: 10.1111/j.1469-0691.2007.01786.x] [Citation(s) in RCA: 530] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For bacterial typing to be useful, the development, validation and appropriate application of typing methods must follow unified criteria. Over a decade ago, ESGEM, the ESCMID (Europen Society for Clinical Microbiology and Infectious Diseases) Study Group on Epidemiological Markers, produced guidelines for optimal use and quality assessment of the then most frequently used typing procedures. We present here an update of these guidelines, taking into account the spectacular increase in the number and quality of typing methods made available over the past decade. Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages. Criteria for their evaluation and application and the interpretation of their results are proposed. Finally, the issues of reporting, standardisation, quality assessment and international networks are discussed. It must be emphasised that typing results can never stand alone and need to be interpreted in the context of all available epidemiological, clinical and demographical data relating to the infectious disease under investigation. A strategic effort on the part of all workers in the field is thus mandatory to combat emerging infectious diseases, as is financial support from national and international granting bodies and health authorities.
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Affiliation(s)
- A van Belkum
- Erasmus MC, Department of Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlands.
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de Melo GB, Aggio FB, Höfling-Lima AL, d'Azevedo PA, Pignatari ACC. Pulsed-field gel electrophoresis in the identification of the origin of bacterial keratitis caused by Pseudomonas aeruginosa. Graefes Arch Clin Exp Ophthalmol 2006; 245:1053-4. [PMID: 17186257 DOI: 10.1007/s00417-006-0503-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2006] [Revised: 10/19/2006] [Accepted: 11/13/2006] [Indexed: 10/23/2022] Open
Abstract
PURPOSE To report the use of pulsed-field gel electrophoresis (PFGE) in the investigation of the origin of infectious keratitis. METHODS A 19-year-old girl presented with infectious keratitis in the left eye. She was a soft contact lens wearer, and was noncompliant with the proper cleaning methods proposed by the manufacturer. Microbiological assessment was performed by means of culture and PFGE. RESULTS The patient was treated successfully with topical cefalotin and gentamicin drops. Cultures were positive for Pseudomonas aeruginosa in the cornea and conjunctiva, and in the contact lens, its case and the cleaning solution. PFGE showed identical patterns of banding in each. CONCLUSION In this case of bacterial keratitis, PFGE proved to be very useful in identifying how the contamination occurred.
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Melo GB, Höfling-Lima AL, Alvarenga LS, Monteiro J, Pignatari ACC. Pulsed field gel electrophoresis of chromosomal bacterial DNA in the investigation of infectious endophthalmitis. Br J Ophthalmol 2006; 90:916-7. [PMID: 16782952 PMCID: PMC1857141 DOI: 10.1136/bjo.2005.088864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Aspergillus spp. have been the subject of numerous epidemiological studies. The most useful typing techniques are DNA based methods including the random amplified polymorphic DNA technique, microsatellite length polymorphisms, restriction fragment length polymorphism (RFLP) analysis using retrotransposon-like sequences as probes, and multilocus sequence typing. The results of typing clinical isolates indicate that most of the invasive aspergillosis (IA) patients were infected by a single strain. Genetic analysis could not discriminate between clinical and environmental isolates of Aspergillus. fumigatus, indicating that every strain present in the environment is a potential pathogen if it encounters the appropriate host. The source of infection can also be monitored by typing. Typing studies led to the discovery of a new pathogenic species, A. lentulus, and to the identification of several species not known previously to be pathogenic. Typing studies revealed the existence of two genetically isolated groups within a global A. fumigatus population. Aspergillus fumigatus was found to be the first example of a true cosmopolitan fungus. Additionally, the results obtained in several studies support the premise that recombination played an important role in A. fumigatus populations. The discovery of functional mating type genes in A. fumigatus indicates that past or recent sexual processes could be responsible for the observed recombining population structure.
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Affiliation(s)
- János Varga
- Department of Microbiology, Faculty of Sciences, University of Szeged, Szeged, Hungary
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Canteros CE, Zuiani MF, Ritacco V, Perrotta DE, Reyes-Montes MR, Granados J, Zúñiga G, Taylor ML, Davel G. Electrophoresis karyotype and chromosome-length polymorphism ofHistoplasma capsulatumclinical isolates from Latin America. ACTA ACUST UNITED AC 2005; 45:423-8. [PMID: 16061363 DOI: 10.1016/j.femsim.2005.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 05/27/2005] [Indexed: 11/30/2022]
Abstract
Intact chromosomes of 19 clinical isolates of Histoplasma capsulatum recently obtained in Argentina, Mexico and Guatemala and the laboratory reference strain G186B from Panama were analyzed using pulsed-field gel electrophoresis. Chromosomal banding patterns of the human isolates revealed 5-7 bands, ranging from 1.3 to 10 Mbp in size. Strain G186B showed five bands of approximately 1.1, 2.8, 3.3, 5.4 and 9.7 Mbp. Thirteen different electrokaryotypes were identified, indicating that the genome of H. capsulatum varies widely in nature, as observed previously in laboratory strains. No definite association was found between electrokaryotype and geographical or clinical source.
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