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A common challenge in pathogen discovery by deep sequencing approaches is to recognize viral or subviral pathogens in samples of diseased tissue that share no significant homology with a known pathogen. Here we report a homology-independent approach for discovering viroids, a distinct class of free circular RNA subviral pathogens that encode no protein and(More)
Complete genomic sequences of nine isolates of sweet potato symptomless virus 1 (SPSMV-1), a virus of the genus Mastrevirus in the family Geminiviridae, were determined from sweet potato accessions from different countries and found to be 2,559-2,602 nucleotides in length. These isolates shared 97-100% genome sequence identity and had an unusual(More)
Antiviral immunity controlled by RNA interference (RNAi) in plants and animals is thought to specifically target only viral RNAs by the virus-derived small interfering RNAs (siRNAs). Here we show that activation of antiviral RNAi in Arabidopsis plants is accompanied by the production of an abundant class of endogenous siRNAs mapped to the exon regions of(More)
Citrus viroid V (CVd-V) was recently characterized and belongs to the genus Apscaviroid within the family Pospiviroidae. 334 CVd-V isolates were identified from Punjab, Pakistan, where CVd-V had not been reported. A total of 68 independent cDNA clones were sequenced from 11 infected trees of different cultivars, ranging from 292 to 295 nucleotides. The(More)
Citrus viroid VI (CVd-VI) is a viroid originally found from citrus and persimmon in Japan. We report here the identification and molecular characterization of CVd-VI from four growth regions of China. A total of 90 cDNA clones from nine citrus cultivars were sequenced. The sequence homologies of the Chinese CVd-VI and the reference sequence (NC_004359) vary(More)
CVd-I-LSS (low sequence similarity), a variant of Citrus bent leaf viroid (CBLVd), was first discovered in Japan, and its distribution is currently limited to Japan and Iran. In the present study, seven CVd-I-LSS isolates were detected from different citrus hosts (Citrus sinensis, C. reticulata and C. limettioides) in Pakistan and China. Genetic diversity(More)
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