Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Abstract

22Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. 23There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short 24interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but comprise only a 25 small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we 26 used a large dataset of published and newly generated sRNA sequencing data (1,333 sRNA-seq 27 libraries containing over 20 billion reads) and a uniform bioinformatic pipeline to produce 28 comprehensive sRNA locus annotations of 47 diverse plants, yielding over 2.7 million sRNA loci. 29The two most numerous classes of siRNA loci produced mainly 24 nucleotide and 21 nucleotide 30 siRNAs, respectively. 24 nucleotide-dominated siRNA loci usually occurred in intergenic regions, 31 especially at the 5'-flanking regions of protein-coding genes. In contrast, 21 nucleotide-32 dominated siRNA loci were most often derived from double-stranded RNA precursors copied 33 from spliced mRNAs. Genic 21 nucleotide-dominated loci were especially common from disease 34 resistance genes, including from a large number of monocots. Individual siRNA sequences of all 35 types showed very little conservation across species, while mature miRNAs were more likely to 36 be conserved. We developed a web server where our data and several search and analysis tools 37 are freely accessible at

Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats

“…Consistent with previous analysis of sRNAs in soybean (Arikit et al, 2014;Lunardon et al, 2020), the majority of siRNA loci in soybean features 24-nt siRNAs, but 21-and 22-nt loci demonstrated higher sRNA abundances ( Figure 2B). In wild-type libraries, our analysis identified 1,304 22-nt siRNA loci from the seed coat and 1,371 from leaf sample, which accounted for only ~3% of the total number of loci but over 20% of total siRNA abundance ( Figure 2B).…”

“…These 22-mers are capable of triggering the production of secondary 21-nt siRNAs to further silence TEs or protein-coding genes. A recent study of sRNAs from 47 diverse plant species showed that many major crops and vegetables produce 22-nt siRNAs at much higher levels compared to Arabidopsis (Lunardon et al, 2020). Our results here demonstrated that DCL2-dependent 22-nt siRNAs are capable of regulating natural traits, and future investigation in more species could help to expand our understanding about the possibly underappreciated function of 22-nt siRNAs in wild-type plants.…”

“…To further analyze these DCL2-dependent siRNAs, we classified sRNA clusters based on the dominant size class in each cluster using ShortStack (Axtell, 2013;Lunardon et al, 2020).…”

“…Loss-of-function of DCL4 in Arabidopsis can induce the production of a large amount of DCL2-dependent 22-nt siRNAs from endogenous genes and cause silencing of their targets, and as a result, plants exhibit various developmental defects (Bouché et al, 2006;Zhang et al, 2015;Wu et al, 2017;Wu et al, 2020). However, endogenous 22-nt siRNAs are abundant in many major crops such as soybean, rice, and maize, indicating their potential importance (Lunardon et al, 2020). For example, 22-nt siRNAs from transposable element (TE) regions are abundant in maize, especially in the mediator of paramutation1-1 (mop1-1) background in which 24-nt siRNAs disappear (Nobuta et al, 2008).…”

MiRNA and phasiRNAs-mediated regulation of TIR-NBS-LRR defense genes inArabidopsis thaliana

“…1; [43, 46]). Using miR825-5p to search for potential target genes in the B. oleareacea genome in a recently created web browser (https://plantsmallrnagenes.science.psu.edu/ ; [77]), we found that several of its predicted targets, which display sequence similarity to Arabidopsis TNL genes, do accumulate significant amounts of 21 nt siRNAs, supporting the potential conservation of miR825-5p TNL regulatory network among Brassicaceae ( Fig. S3 ).…”