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Switt AIM, Sulakvelidze A, Wiedmann M, Kropinski AM, Wishart DS, Poppe C, Liang Y. Salmonella phages and prophages: genomics, taxonomy, and applied aspects. Methods Mol Biol 2015; 1225:237-87. [PMID: 25253259 DOI: 10.1007/978-1-4939-1625-2_15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.
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Affiliation(s)
- Andrea I Moreno Switt
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Escuela de Medicina Veterinaria, Republica 440, 8370251, Santiago, Chile
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Periwal V, Scaria V. Insights into structural variations and genome rearrangements in prokaryotic genomes. ACTA ACUST UNITED AC 2014; 31:1-9. [PMID: 25189783 DOI: 10.1093/bioinformatics/btu600] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.
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Affiliation(s)
- Vinita Periwal
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007 and Academy of Scientific & Innovative Research (AcSIR), Anusandhan Bhawan, New Delhi 110001, India
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Turner D, Reynolds D, Seto D, Mahadevan P. CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Res Notes 2013; 6:140. [PMID: 23566564 PMCID: PMC3630060 DOI: 10.1186/1756-0500-6-140] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes. Findings CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format. Conclusions With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at http://binf.gmu.edu:8080/CoreGenes3.5.
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Affiliation(s)
- Dann Turner
- Centre for Research in Biosciences, Faculty of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
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Mahadevan P, Seto D. In silico bioinformatic tools for determining core genes from sets of genomes. Drug Dev Res 2010. [DOI: 10.1002/ddr.20411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mahadevan P, Seto D. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. BMC Res Notes 2010; 3:41. [PMID: 20178631 PMCID: PMC2844394 DOI: 10.1186/1756-0500-3-41] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 02/23/2010] [Indexed: 11/30/2022] Open
Abstract
Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations. Conclusions The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.
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Affiliation(s)
- Padmanabhan Mahadevan
- Department of Bioinformatics and Computational Biology, 10900 University Blvd,, MSN 5B3, George Mason University, Manassas, VA 20110, USA.
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Abstract
One of the most satisfying aspects of a genome sequencing project is the identification of the genes contained within it.These are of two types: those which encode tRNAs and those which produce proteins. After a general introduction on the properties of protein-encoding genes and the utility of the Basic Local Alignment Search Tool (BLASTX) to identify genes through homologs, a variety of tools are discussed by their creators. These include for genome annotation: GeneMark, Artemis, and BASys; and, for genome comparisons: Artemis Comparison Tool (ACT), Mauve, CoreGenes, and GeneOrder.
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Commins J, Toft C, Fares MA. Computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. Biol Proced Online 2009; 11:52-78. [PMID: 19495914 PMCID: PMC3055744 DOI: 10.1007/s12575-009-9004-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 02/17/2009] [Indexed: 12/02/2022] Open
Abstract
Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. Despite many advances made in such endeavor, the ever-lasting annoying exceptions to the general patterns remain to pose difficulties in generalizing methods for comparative genomics. In this review, we discuss the different tools devised to undertake the challenge of comparative genomics and some of the exceptions that compromise the generality of such methods. We focus on endosymbiotic bacteria of insects because of their genomic dynamics peculiarities when compared to free-living organisms.
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Affiliation(s)
- Jennifer Commins
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
| | - Christina Toft
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
| | - Mario A Fares
- Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
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Galperin MY, Kolker E. New metrics for comparative genomics. Curr Opin Biotechnol 2006; 17:440-7. [PMID: 16978854 PMCID: PMC1764326 DOI: 10.1016/j.copbio.2006.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/10/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
The availability of genome sequences from a variety of organisms presents an opportunity to apply this sequence information to solving the key problems of molecular biology. One of the principal roadblocks on this path is the lack of appropriate descriptors and metrics that could succinctly represent the new knowledge stemming from the genomic data. Several new metrics have recently been used in comparative genome analysis, yet challenges remain in finding an appropriate language for the emerging discipline of systems biology.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and
- Corresponding authors: Galperin, Michael Y (); Kolker, Eugene ()
| | - Eugene Kolker
- The BIATECH Institute, 19310 North Creek Pkwy, Suite 115, Bothell, WA 98011, USA
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Esteban DJ, Da Silva M, Upton C. New bioinformatics tools for viral genome analyses at Viral Bioinformatics--Canada. Pharmacogenomics 2006; 6:271-80. [PMID: 16013958 DOI: 10.1517/14622416.6.3.271] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Viruses are much smaller than prokaryotes and eukaryotes, and it is now practical to sequence closely related members of virus families, strains, or even different isolates recovered during the course of an outbreak. However, comparative analysis of viral genomes requires the development of novel bioinformatics tools that allow us to align, edit, compare and interact with these genomes at all levels, from whole genome, to gene family, to single nucleotide polymorphisms. Comparative viral genomics can lead to the identification of the core characteristics that define a virus family, as well as the unique properties of viral species or isolates that contribute to variations in pathogenesis. This paper describes a number of tools, mainly developed for Viral Bioinformatics--Canada, that can be used for annotation and comparative genomic analysis of poxviruses. Nonetheless, these tools are also broadly applicable to other virus families.
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Affiliation(s)
- David J Esteban
- University of Victoria, Department of Biochemistry and Microbiology, Victoria, BC V8W 3P6, Canada.
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Abstract
MOTIVATION Establishment of intra-cellular life involved a profound re-configuration of the genetic characteristics of bacteria, including genome reduction and rearrangements. Understanding the mechanisms underlying these phenomena will shed light on the genome rearrangements essential for the development of an intra-cellular lifestyle. Comparison of genomes with differences in their sizes poses statistical as well as computational problems. Little efforts have been made to develop flexible computational tools with which to analyse genome reduction and rearrangements. RESULTS Investigation of genome reduction and rearrangements in endosymbionts using a novel computational tool (GRAST) identified gathering of genes with similar functions. Conserved clusters of functionally related genes (CGSCs) were detected. Heterogeneous gene and gene cluster non-functionalization/loss are identified between genome regions, functional gene categories and during evolution. Results show that gene non-functionalisation has accelerated during the last 50 MY of Buchnera's evolution while CGSCs have been static.
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Affiliation(s)
- Christina Toft
- Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth
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