PURPOSE Here we describe LifePrint, a sequence alignment-independent k-tuple distance method to estimate relatedness between complete genomes. METHODS We designed a representative sample of all possible DNA tuples of length 9 (9-tuples). The final sample comprises 1878 tuples (called the LifePrint set of 9-tuples; LPS9) that are distinct from each other by at least two internal and noncontigu...

Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants (Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae, ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5-hydroxyl and 2,3-cyclic phosphodiester groups. Available experimenta...

This is the first report of chrysanthemum virus B (CVB) and chlorotic mottle viroid (CChMVd) on Chrysanthemum × morifolium cultivars, in South Africa. Samples were collected from plants showing vein clearing, mosaic chlorosis, Western Cape province. RNAtag-seq was applied indicated presence CVB all four samples co-infection with CChMVd one sample. The confirmed using RT-PCR Sanger sequencing.

Due to their small size, locating pathogenic RNAs, such as viroids, in plant tissue and cell organelles has been difficult. Viroids are circular single-stranded RNA virus-like pathogens that reduce growth, vigor, yield economically important crops potato, tomato, hops citrus. Viroid infections plants largely diagnosed by dot blot hybridization, PAGE-gels, or RT-PCR. Because traditional situ hyb...

Grapevine yellow speckle viroid 1 (GYSVd1), which is a member of the genus Apscaviroid, causes yellow speckle disease in grapevines. Here, we report the complete de novo genome assembly of GYSVd1 from the grapevine transcriptome and identified 10 single nucleotide polymorphisms of GYSVd1 across the grapevine populations.

The transcription initiation sites of viroid RNAs, despite their relevance for replication and in vivo folding, are poorly characterized. Here we have examined this question for Peach latent mosaic viroid (PLMVd), which belongs to the family of chloroplastic viroids with hammerhead ribozymes (Avsunviroidae), by adapting an RNA ligase-mediated rapid amplification of cDNA ends methodology develop...

We have developed an electroporation protocol to inoculate cultured cells of tobacco and Nicotiana benthamiana with in vitro transcripts of Potato spindle tuber viroid (PSTVd) to characterize viroid structural features that determine replication efficiency at the cellular level. Both (+)- and (-)-strands of PSTVd were detected by Northern blots as early as 6 h postinoculation (h.p.i.). Accumula...

RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of ...