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Genome Sequencing

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Phytoplasmas: Plant Pathogenic Bacteria - III

Abstract

Genome sequences are of major importance to phytoplasma research, as they provide the blueprint for understanding evolution, metabolism and virulence factors of phytoplasmas. Genome projects on these obligate parasites start from metagenomic templates taken from colonised plant- or insect-vector material, meaning that they have to deal with high amounts of untargeted DNA. This problem separates phytoplasmas from the majority of other bacterial genome projects, and methodological approaches deal with it by using strong colonised tissues and enriching phytoplasma DNA. The impact of this situation was severe for the first genome projects using Sanger sequencing, while the most recent phytoplasma genome projects have tried to overcome the problem through huge amounts of reads derived from next-generation sequencing approaches, thus enabling the generation of draft sequences or even complete phytoplasma genomes. Genomic sequence determination is hampered by their repeat-rich content, resulting in conflicts during the sequence assemblies in addition. An overview is provided of the strategies applied to phytoplasma genome sequencing and data processing, as well as currently available data on these particular bacteria.

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Author information

Authors and Affiliations

  1. Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany

    Michael Kube

  2. Institute of Pesticides and Environmental Protection, Belgrade, Serbia

    Bojan Duduk

  3. Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan

    Kenro Oshima

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  1. Michael Kube
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  2. Bojan Duduk
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Editors and Affiliations

  1. Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Bologna, Italy

    Assunta Bertaccini

  2. Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo, Japan

    Kenro Oshima

  3. Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany

    Michael Kube

  4. Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India

    Govind Pratap Rao

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Kube, M., Duduk, B., Oshima, K. (2019). Genome Sequencing. In: Bertaccini, A., Oshima, K., Kube, M., Rao, G. (eds) Phytoplasmas: Plant Pathogenic Bacteria - III. Springer, Singapore. https://doi.org/10.1007/978-981-13-9632-8_1

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