Two novel variants of hop stunt viroid associated with yellow corky vein disease of sweet orange and split bark disorder of sweet lime

Abstract

Yellow corky vein was reported as a graft-transmissible disease of lime in India. It was attributed to infection by hop stunt viroid (HSVd) and citrus exocortis viroid (CEVd). Recently similar symptoms have been observed in Washington navel orange in Jahrom and Darab in the Fars province of Iran. It is characterized by yellowing and suberization of veins followed by tree decline. Sweet lime split bark is another disorder of increasing importance in the Fars province. It is characterized by cracks in the bark of the main stem which may spread to branches of the tree. Since these symptoms resembled those of certain viroids, a study was undertaken to determine possible association of viroids with the disorders. Reverse transcription polymerase chain reaction (RT-PCR) followed by cloning and sequencing of PCR products and dot-blot hybridization were used to identify the viroids associated with the diseases. Comparison of molecular properties (nucleotide composition, primary and secondary structures, molecular weights, phylogenetic relationships and percent nucleotide similarity and difference) of viroid variants were carried out. It was found that a novel variant of hop stunt viroid (HSVd-sycv) was associated with yellow corky vein disease of Washington navel and another new variant (HSVd-sb) with split bark disorder of sweet lime. No other viroids were constantly detected. HSVd-sycv was closely related to noncachexia variant of hop stunt viroid (HSVd-cit) but only with 93.7% homology with HSVd-lycv. It differed in a single nucleotide from HSVd-cit, in the variable domain in the so-called “cachexia expression motif”. HSVd-sb had only 94.8% homology with a noncachexia variant of hop stunt viroid (CVd-IIa-117) which causes mild bark-cracking symptoms on Pomeroy trifoliate orange rootstocks. According to the performed molecular comparisons, HSVd-sb differed from CVd-IIa-117 in “cachexia expression motif” and probably severe cracks induced by HSVd-sb occurred because of variation in this motif.

Keyword: HSVd, Sweet lime split bark, Sweet orange yellow corky vein, Citrus viroids, Viroid phylogeny