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Title: Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis

Author
item Lee, Ing Ming
item Bottner, Kristi
item Zhao, Yan
item BERTACCINI, A - University Of Bologna
item Davis, Robert

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/13/2012
Publication Date: 2/3/2012
Citation: Lee, I., Bottner-Parker, K.D., Zhao, Y., Bertaccini, A., Davis, R.E. 2012. Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis. International Journal of Systematic and Evolutionary Microbiology. 62:2279-2285.

Interpretive Summary: Phytoplasmas are very small bacteria that lack a cell wall and that cause several hundred economically important diseases in plants including food and vegetable crops, such as potato, sweet potato, corn, bean, tomato, carrot; small fruit crops, grapevine, blueberry, blackberry, strawberry; fruit trees, cherry, peach, apple, pear; and forest trees, elm, palm, juniper, and ash. More than 1000 phytoplasma strains have been reported to be associated with various diseases worldwide. The different phytoplasmas attacking these plants, in many cases, are closely related to each other, and it has been difficult to distinguish them from one another by molecular mean using a highly conserved gene, ribosomal RNA as a biomarker. Some of these closely related strains possess unique biological and ecological properties, causing different diseases in specific geographical regions. For quarantine purpose, it is essential to develop a molecular tool that allows for the identification of such strains. We studied less conserved genes such as ribosomal (rp) genes and a translocation protein gene, secY, as additional molecular markers for identifying closely related phytoplasmas. Analysis of these genes proved very useful for finer phytoplasma strain differentiation and identification of closely related but distinct phytoplasma strains. The information will interest scientists, students, diagnosticians and extension workers. It will facilitate epidemiological studies and aid implementation of quarantine regulation, and it will help extension workers and plant diagnosticians to determine how to combat the disease.

Technical Abstract: Pigeon pea witches’-broom phytoplasma group (16SrIX) consists of diverse phytoplasma strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree, and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses with the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)-rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these distinct lineages cannot be readily differentiated based on analysis of 16SrRNA gene sequences alone. Their relative genetic distances among these closely related lineages were better assessed by including additional more variable genes (e.g. rp and secY genes). The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A cording system was proposed to designate each of distinct rp and secY subgroups, respectively, in the 16SrIX group.