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Genome Sequencing

  • Michael Kube
  • Bojan Duduk
  • Kenro Oshima
Chapter

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.

Keywords

NGS Complete genomes Draft sequences Genome instability 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Michael Kube
    • 1
  • Bojan Duduk
    • 2
  • Kenro Oshima
    • 3
  1. 1.Integrative Infection Biology Crops-LivestockUniversity of HohenheimStuttgartGermany
  2. 2.Institute of Pesticides and Environmental ProtectionBelgradeSerbia
  3. 3.Department of Clinical Plant Science, Faculty of Bioscience and Applied ChemistryHosei UniversityTokyoJapan

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