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

Abstract

Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24-and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5 ′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

“…The miRNA sequence data are mostly derived from miRBase (release 22) [ 43 ]. Some miRNA data are from PmiREN [ 44 ] and Plant sRNA Gene server [ 50 ]. Users can view the sequences and secondary structures of mature/precursor miRNAs, and click on the corresponding external links to obtain more miRNA information (Fig.…”

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

“…More recently, comparison of gene expression in wild type and pol IV mutant plants from two Brassicaceae species ( A. thaliana and C. rubella ) found only negligible overlap in RdDM-targeted genes [ 119 ]. Unlike the many cases of ancient plant miRNA–target mRNA pairs, Pol IV-dependent siRNAs rarely target genes in an evolutionary conserved manner across species [ 158 , 159 ]. Instead, the dynamic reprogramming of gene expression via RdDM, observed under stress conditions [ 122 , 160 ] and during key phases in reproduction [ 161–164 ] may allow plants to evolve and adapt to challenging conditions in a stochastic manner over shorter timescales.…”

MIR172d Is Required for Floral Organ Identity and Number in Tomato

“…MiR172 is highly conserved in seed plants, but was not identified in more ancient plant clades such as lycopods and bryophytes [ 5 ]. The miR172 family was identified in at least 30 angiosperm species and contains up to 11 members ( Glycine max ) [ 6 ]. MiR172 targets mRNAs that encode euphyllophyte APETALA2 (euAP2) transcription factors, a lineage of the AP2/ethylene responsive factor (ERF) superfamily, by both transcript cleavage as well as by translational inhibition mechanisms [ 7 , 8 ].…”