Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences

• Published in: International journal of systematic and evolutionary microbiology Vol. 60; no. Pt 12; pp. 2887 - 2897
• Main Authors: LEE, I.-M, BOTTNER-PARKER, K. D, ZHAO, Y, DAVIS, R. E, HARRISON, N. A
• Format: Journal Article
• Language: English
• Published: Reading Society for General Microbiology 01.12.2010
• Subjects: Bacterial Typing Techniques; Bacteriology; Base Sequence; Biological and medical sciences; DNA, Bacterial - genetics; Fundamental and applied biological sciences. Psychology; Genes, Bacterial; Microbiology; Molecular Sequence Data; Operon; Phylogeny; Phytoplasma - classification; Phytoplasma - genetics; Phytoplasma - isolation & purification; Polymorphism, Restriction Fragment Length; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Systematics; Mollicutes; Plant pathogen; Nucleotide sequence; Taxonomy; Bacteria; Phylogeny; Phytoplasma
• ISSN: 1466-5026; 1466-5034; 1466-5034
• DOI: 10.1099/ijs.0.019695-0

The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the secY gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective secY RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.