nucleotide sequence and structural features of hop stunt viroid and citrus bent leaf viroid variants from blighted citrus plants in kohgiluyeh–boyerahmad province of iran

hop stunt viroid (hsvd) isolates have been reported as the causal agent of citrus cachexia in mazandaran province and recently shown to be associated with yellow corky vein disease of sweet orange and split bark disorder of sweet lime in the fars province, iran. in the present work isolation and partial characterization of viroids from citrus trees affected by gummy stem blight is reported from kohgiluyeh–boyerahmad (kb) province of iran. fifteen samples of citrus trees from dehdasht area (kb province) showing bark necrosis, gum exudation and die-back as well as seven citrus symptompless trees from the same area were tested for the prevalence of viroids, through reverse transcription polymerase chain reaction (rt-pcr) followed by sequencing of pcr products. they were also tested for citrus tristeza virus through double-antibody sandwich enzyme linked immunosorbent assay (das-elisa). two variants of hsvd which differed from genbank isolates in nucleotide sequence and two variants of citrus bent leaf viroid (cblvd) were identified in any of the symptomatic samples. moreover, a citrus exocortis viroid (cevd) was found only in symptomatic sweet lime. an hsvd isolate from kb (hsvd-bn1) was selected and used for comparison with a number of hsvd variants from iran (fars and mazandaran provinces) and the related accessions from genbank. on the basis of nucleotide sequence and secondary structure analysis, hsvd-bn1 and hsvd-bn2 belong to non-cachexia variants of hsvd and have about 95% similarity to citrus gummy bark viroid, a sub-species of hsvd. ctv was not detected in the diseased plants. it is yet to be determined whether bark necrosis of sweet lime and of sweet orange plants is caused solely by the associated viroid(s) or other factors are involved as well.