Abstract
Viroids are circular, highly structured, single-stranded, non-coding RNA pathogens known to infect and cause disease in several plant species. They are known to trigger the host plant’s RNA silencing machinery. The detection of viroid-derived small RNAs (vd-sRNA) in viroid-infected host plants opened a new avenue of study in host–viroid pathogenicity. Since then, several viroid research groups have studied the vd-sRNA retrieved from different host–viroid combinations. Such studies require the segregation of 21- to 24-nucleotide long small RNAs (sRNA) from a deep-sequencing databank, followed by separating the vd-sRNA from any sRNA within this group that showed sequence similarity with either the genomic or the antigenomic strands of the viroid. Such mapped vd-sRNAs are then profiled on both the viroid’s genomic and antigenomic strands for visualization. Although several commercial interfaces are currently available for this purpose, they are all programmed for linear RNA molecules. Hence, viroid researchers must develop a computer program that accommodates the sRNAs derived from the circular viroid genome. This is a laborious process, and consequently, it often creates a bottleneck for biologists. In order to overcome this constraint, and to help the research community in general, in this study, a python-based pattern matching interface was developed so as to be able to both profile and map sRNAs on a circular genome. A “matching tolerance” feature has been included in the program, thus permitting the mapping of the sRNAs derived from the quasi-species. Additionally, the “topology” feature allows the researcher to profile sRNA derived from both linear and circular RNA molecules. The efficiency of the program was tested using previously reported deep-sequencing data obtained from two independent studies. Clearly, this novel software should be a key tool with which to both evaluate the production of sRNA and to profile them on their target RNA species, irrespective of the topology of the target RNA molecule.
Highlights
IntroductionViroids are both the simplest and the smallest known plant pathogens
Upon infection, all viroids trigger RNA silencing, and this results in the cleavage of the viroid RNA into small RNAs (sRNA) of 21- to 24-nts in length. The accumulation of these viroid-derived small RNAs (vd-sRNA) has been extensively studied in different host–viroid combinations [10,11,13]
Included in these studies was the prediction of the vd-sRNA:target mRNA duplex formation and searching for the number of vd-sRNAs in the viroid-infected plant that could potentially bind to a given target mRNA
Summary
Viroids are both the simplest and the smallest known plant pathogens. Since viroids do not encode for any known peptides, they rely entirely on their sequence, structure and host factors in order to replicate and induce disease symptoms in their host plants. Upon infection, they induce a wide array of symptoms in their host plants, such as leaf epinasty, leaf distortion, stunting and flower distortion [2,3,4]. Due to both their highly base-paired secondary structures and their RNA-RNA mode of replication, viroids are both inducers and targets of RNA silencing [5]
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