The Multiverse of Plant Small RNAs: How Can We Explore It?

Abstract

Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.

Exogenous Application of dsRNA for the Control of Viruses in Cucurbits

“…It is mediated mainly by two types of molecules, small-interfering RNAs (siRNAs) and microRNAs (miRNAs) (Sanan-Mishra et al, 2021 ). Whereas, the former is endogenously-derived and involved in the regulation of gene expression, small RNAs can be of exogenous origin from viruses or artificial supply (Matranga and Zamore, 2007 ), endogenous derived from transposons (Golden et al, 2008 ), from overlapping transcripts, such as natural antisense siRNAs (nat-siRNAs), or secondary siRNAs-phased siRNAs (phasiRNAs), and transacting siRNAs (tasiRNAs) (Ivanova et al, 2022 ). The presence of exogenous double-stranded RNA (dsRNA) generates the activation of DICER and RISC complexes that cleave dsRNA and use the siRNAs as a template for the degradation of complementary RNAs (Vargason et al, 2003 ; Pantaleo et al, 2007 ).…”

A pipeline for validation of sRNA effectors suggests cross-kingdom communication in the symbiosis ofArabidopsiswithSerendipita indica

“…High throughput sequencing of samples from the Si-Ath interaction including transcriptional analysis and degradome sequencing are needed to better understand Si sRNA-mediated target cleavage. Moreover, consideration for sRNA non-canonical cleavage site may also be further investigated as different studies speculate that PTGS can still be induced through sRNA or phasiRNA and generate a non-canonical cleavage site (Brousse et al ., 2014; Ivanova et al ., 2022).…”

The Fascinating World of Plant Non-Coding RNAs

“…In addition to the research papers, several review studies in the field of miRNA roles in plant stress responses and medicinal plants [ 9 , 10 ], as well as bioinformatics approaches for identification of isomiRs [ 11 ], further extend and augment the knowledge in the ncRNAs literature, making them valuable addition to this Special Issue.…”