Phytoplasma pp 319-327 | Cite as

Phylogenetic Analyses of Phytoplasmas Based on Whole-Genome Comparison

  • Hiromi NishidaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 938)


It is no longer as difficult to determine genomic DNA sequences of uncultured bacteria as it once was, due to the development of DNA sequencing technology. It is likely that the number of whole-genome sequences of phytoplasmas will increase. In this chapter, two major strategies of whole-genome comparison studies, viz. gene content and orthologous protein sequence comparisons, are described. In general, horizontal gene transfer has greater influence on gene content-based phylogenetic analysis than orthologous protein sequence-based analysis. However, horizontal gene transfer has occurred rarely during the evolution of Mollicutes. Thus, the two phylogenetic topologies of the Mollicutes based on the two different strategies are similar.

Key words

Gene content comparison Mollicutes Mycoplasma Orthologous protein sequence comparison 


  1. 1.
    Alam MT et al (2010) Genome-based phylogenetic analysis of Streptomyces and its relatives. Mol Phylogenet Evol 54:763–772PubMedCrossRefGoogle Scholar
  2. 2.
    Oshima K et al (2011) Unique evolution of Symbiobacterium thermophilum suggested from gene content and orthologous protein sequence comparisons. Int J Evol Biol 2011:376831Google Scholar
  3. 3.
    Wolf YI et al (2002) Genome trees and the tree of life. Trends Genet 18:472–479PubMedCrossRefGoogle Scholar
  4. 4.
    Oshima K, Nishida H (2007) Phylogenetic relationships among mycoplasmas based on the whole genomic information. J Mol Evol 65:249–258PubMedCrossRefGoogle Scholar
  5. 5.
    Oshima K, Nishida H (2008) Detection of the genes evolving under Ureaplasma-specific selection. J Mol Evol 66:529–532PubMedCrossRefGoogle Scholar
  6. 6.
    Uchiyama I, Higuchi T, Kawai M (2010) MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. Nucl Acids Res 38:D361–D365PubMedCrossRefGoogle Scholar
  7. 7.
    Tamura K et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCrossRefGoogle Scholar
  8. 8.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  9. 9.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797PubMedCrossRefGoogle Scholar
  10. 10.
    Dickinson M (2010) Mobile units of DNA in phytoplasma genomes. Mol Microbiol 77:1351–1353PubMedCrossRefGoogle Scholar
  11. 11.
    Bai X et al (2006) Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol 188:3682–3696PubMedCrossRefGoogle Scholar
  12. 12.
    Wei W et al (2008) Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution. PNAS USA 105:11827–11832PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan

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