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Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2242))

Abstract

High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.

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Acknowledgments

The sequencing and comparative genomics analyses were funded from National Science Centre in Poland via 2014/14/M/NZ8/00501 granted to EL. National Science Centre in Poland via grant 2016/21/N/NZ1/02783 is currently supporting the work of AMP. The authors are highly grateful to Dr. Michal Kabza for provision of the script for genome reorientation, written in Python language.

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  1. Sabina Zoledowska

    Present address: Institute of Biotechnology and Molecular Medicine, Gdansk, 3 Trzy Lipy, Poland

Authors and Affiliations

  1. Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland

    Sabina Zoledowska, Agata Motyka-Pomagruk, Agnieszka Misztak & Ewa Lojkowska

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  1. Sabina Zoledowska
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  2. Agata Motyka-Pomagruk
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  3. Agnieszka Misztak
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Correspondence to Ewa Lojkowska .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Alessio Mengoni

  2. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Giovanni Bacci

  3. Department of Biology, University of Florence, Sesto Fiorentino, Firenze, Italy

    Marco Fondi

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Zoledowska, S., Motyka-Pomagruk, A., Misztak, A., Lojkowska, E. (2021). Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. In: Mengoni, A., Bacci, G., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 2242. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1099-2_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1099-2_7

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