sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling

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 vdsRNAs 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.

Viroids, Satellite RNAs and Prions: Folding of Nucleic Acids and Misfolding of Proteins

“…Consequently, we cannot forget the pioneering work of Theodor O. Diener and his successors: Joseph S. Semancik [ 69 ] and Heinz L. Sänger [ 70 ], who described first the citrus exocortis viroid; Rudra P. Singh and his work on PSTVd [ 103 ]; John W. Randles and his discovery of CCCVd [ 31 , 32 ]; and Robert H. Symons, who first described the ASBVd and its self-splicing by hammerhead ribozymes [ 28 , 104 ]. The discovery of new viroid(-like) RNAs has increased in recent years mostly due to the use of high-throughput sequencing [ 105 , 106 , 107 , 108 ].…”

CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes

“…Early efforts in developing tools for these genomes often involved intricate workflows, integrating numerous tools coded in diverse programming languages, making them less accessible, especially for non-bioinformaticians. While recent advancements have introduced tools for aligning reads to circular genomes ( Ayad & Pissis, 2017 ; Adkar-Purushothama et al ., 2021 ), sophisticated programming skills are still needed owing to limited documentation and illustrative examples.…”

CircSeqAlignTk: An R package for end-to-end analysis of RNA-seq data for circular genomes

“…Early efforts in developing tools to cater to such genomes often relied on complex workflows that involved a large number of tools written in different programming languages and were thus not user friendly, especially for non-bioinformaticians. Although several tools have recently been developed for aligning reads to circular genomes (Ayad & Pissis, 2017;Adkar-Purushothama et al, 2021), these tools often require advanced programming skills to compensate for a lack of rich documentation and example usage.…”