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A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

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Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses.

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Acknowledgments

This work was supported by a project from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES-BIGA, number 3385/2013). DOA was supported by a postdoctoral research fellowship from the São Paulo Research Foundation (FAPESP n° 2015/14600-5).

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Authors and Affiliations

  1. Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”–UNESP, Jaboticabal, SP, Brazil

    Danillo Oliveira Alvarenga & Alessandro M. Varani

  2. Departamento de Ciências Biológicas–Núcleo de Pesquisas em Ciências Biológicas-NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil

    Leandro M. Moreira

  3. Laboratoire de Microbiologie et Génétique Moléculaires, CNRS 118, Route de Narbonne, 31062, Toulouse Cedex, France

    Mick Chandler

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  1. Danillo Oliveira Alvarenga
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  2. Leandro M. Moreira
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  3. Mick Chandler
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  4. Alessandro M. Varani
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Corresponding author

Correspondence to Alessandro M. Varani .

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Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

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Oliveira Alvarenga, D., Moreira, L.M., Chandler, M., Varani, A.M. (2018). A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes. In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_7

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