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

Part of the Methods in Molecular Biology book series (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.

Key words

  • Transposons
  • Insertion sequences
  • Prophages
  • Clustered regularly interspaced short palindromic repeats
  • Genomic islands
  • Integrons
  • Integrative conjugative elements
  • Evolution
  • Genomics

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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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Correspondence to Alessandro M. Varani .

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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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