Molecular Plant Pathology Laboratory (MPPL)
Two systems for classification of phytoplasmas:
There are two major systems for classification of phytoplasmas. Both systems are based on the analysis of phytoplasma genes, mainly 16S rRNA genes. It is often desirable to classify a phytoplasma strain according to both systems.
I. 16Sr groups and subgroups.
In the first system, phytoplasma are classified into groups and subgroups, based on the "fingerprint" of a segment of the gene that encodes 16S rRNA. In this system, each phytoplasma group is designated by a Roman numeral, and each subgroup is designated by a capital letter. The "fingerprint" consists of the RFLP** patterns is obtained by digesting a special segment of the gene (DNA) with enzymes (restriction endonucleases), each of which cuts a DNA molecule at a specific sequence (recognition site) of 4 or 6 nucleotides. After digestion, the DNA consists of a mixture of different sized fragments, which is then analyzed by electrophoresis through a gel. Gel electrophoresis results in separation of the fragments according to their sizes, the smaller fragments traveling faster (and farther in a given time) than the larger fragments. The bands of DNA fragments in the gel can be seen by the use of special DNA staining methods and then can be photographed. Similarities in the RFLP patterns among the DNAs from different phytoplasmas can be calculated and expressed as similarity coefficients. The level of similarity between two different phytoplasmas determines whether they will both be classified as in the same group (16Sr group) or in different groups. If the two phytoplasmas belong to the same group, the similarity coefficient will determine whether they belong to the same subgroup or different subgroups in that group.
If the nucleotide sequence of the 16S rRNA gene is known for an unclassified phytoplasma, it is possible to obtain a "virtual" RFLP pattern of the DNA and automated calculation of similarity coefficients. This analysis can determine the 16Sr group and subgroup of an unclassified phytoplasma. (See iPhyClassifier at web site).
In the second system, phytoplasmas are classified into 'Candidatus Phytoplasma' species, based on the nucleotide sequence of the 16S rRNA gene. (LINK TO II. 'Candidatus Phytoplasma' species section).
**RFLP, restriction fragment length polymorphism
Dr. Robert E. Davis, Research Leader
United States Department of Agriculture Building 004, BARC-West
10300 Baltimore Ave. Beltsville, MD. 20705
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