Phylogenetic positions of ‘Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins
Open Access
- 1 September 2005
- journal article
- Published by Microbiology Society in International Journal of Systematic and Evolutionary Microbiology
- Vol. 55 (5), 2131-2141
- https://doi.org/10.1099/ijs.0.63655-0
Abstract
Phytopathogenic mollicutes, which include spiroplasmas and phytoplasmas, are cell wall-less bacteria that parasitize plant hosts and insect vectors. Knowledge of the evolution of these agents is important in understanding their biology. The availability of the first complete phytoplasma and several partial spiroplasma and phytoplasma genome sequences made possible an investigation of evolutionary relationships between phytopathogenic mollicutes and other micro-organisms, especially Gram-positive bacteria, using a comparative genomics approach. Genome data from a total of 41 bacterial species were used in the analysis. Sixty-one conserved proteins were selected from each species for the construction of a hypothetical phylogenetic tree. The genes encoding these selected proteins are among a core of genetic elements that constitute a hypothetical minimal genome. The proteins were concatenated into five superproteins according to their functional categories, and phylogenetic trees were reconstructed using distance, parsimony and likelihood methods. Phylogenetic trees based on the five sets of concatenated proteins were congruent in both clade topology and relative branching length. Spiroplasma kunkelii and phytoplasmas clustered together with other mollicutes, forming a monophyletic group. Phytoplasmas diverged from spiroplasmas and mycoplasmas at early stages in the evolution of mollicutes. Branch lengths on the phylogenetic trees were noticeably longer in the Mollicutes clade, suggesting that the genes encoding the five sets of proteins evolved at a greater rate in this clade than in other clades. This observation reinforces the concept that mollicutes have rapidly evolving genomes.Keywords
This publication has 46 references indexed in Scilit:
- The genus Spiroplasma and its non-helical descendants: phylogenetic classification, correlation with phenotype and roots of the Mycoplasma mycoides cladeInternational Journal of Systematic and Evolutionary Microbiology, 2004
- Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence dataInternational Journal of Systematic and Evolutionary Microbiology, 2004
- Temporal Changes in Phosphoglycerate Kinase Coding Sequences: A Quantitative MeasureJournal of Computational Biology, 2003
- A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common HistoryGenome Research, 2002
- The evolutionary history of ribosomal protein RpS14:: horizontal gene transfer at the heart of the ribosomeTrends in Genetics, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- The Comparative Metabolism of the Mollicutes (Mycoplasmas): The Utility for Taxonomic Classification and the Relationship of Putative Gene Annotation and Phylogeny to Enzymatic Function in the Smallest Free-Living CellsCritical Reviews in Microbiology, 1997
- Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in BacteriologyInternational Journal of Systematic and Evolutionary Microbiology, 1994
- The rapid generation of mutation data matrices from protein sequencesBioinformatics, 1992
- Cloning and cDNA sequence of the rat X-chromosome linked phosphoglycerate kinaseBiochemical and Biophysical Research Communications, 1989