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Many investigations have confnrmed that the abundant genetic diversity of phytoplasmas is associated with their adaptation to ecological condition and pathogenicity to plant hosts and insect vectors.The structural diversity and sequence polymorphisms upstream to tufgene(encoding elongation factor EF-Tu)of 31strains of 16SrI group phytoplasma from 15 provinces,including 18 paulownia witches-broom phytoplasma(PaWB)strains,nine chinaberry witehes-broom phytoplasma(CWB)strains,two lettuce yellows phytoplasma(LY)strains,one mulberry dwarf phytoplasma(MD)strain and one periwinkle virescence phytoplasma(PeV)strain,and 18 strains of 16SrV group phytoplasma from nine provinces,including 15 jujube witches-broom phytoplasma(JWB)strains,one Bischofia polycarpa witehes-broom phytoplasma(BiWB),Sophorajaponica witches-broom phytoplasma(SoWB)and cherry lethal yellow phytoplasma(CLY)strain,were revealed by the method of direct/TAIL-PCR and genetic analysis in the study.The results showed that the length of intergenic region(IR)betweenfusA and tufgenes was 129 to 130bp in 16SrI group strains and 53 to 54 bpin 16SrV group strains respectively.The putative promoters in IR of f usA and tufin 16SrI group strains were predicted while those in 16SrV group strains were absent.Specific to the IR sequences,there were four kinds of variable types with four variable sites in 16SrI group strains which related to the plant hosts.However,one variable site,transversion between A and C,existed between the unique PaWB strain from Fuzhou,Fujian province and all the PaWB isolates from other provinces in the promoter sequences.Two kinds of variable types with only one variable site were found in the IR sequences of 16SrV group strains.There was an A insertion in the sequence of JWB from Puyang,Henan province and SoWB from Beijing.The putative Shine-Dalgamo(SD)sequence in both 16SrI and V group strains was a highly conserved region 5-AGGAGGC-3.The findings suggested that the diversity of gene arrangement and complexity of gene regulation as well as the comparatively conserved sequence property in diverse phytoplasmas could also be employed to develop some potential methods for identifying and differentiating different phytoplasma strains.