An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

Abstract

Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNAdependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets.

The pivotal role of small non-coding RNAs in the regulation of seed development

“…Consistently with this hypothesis, the abundance of total 24-nt reads seems to decrease as seed develops, in both eudicots such as canola (Huang et al 2013) and monocots such as barley (Curaba et al 2012), rice (Peng et al 2013) and wheat (Table 1). A further decrease after seed germination has also been observed in soybean, where the number of 24-nt distinct sRNA is higher in immature cotyledons (Zabala et al 2012;Arikit et al 2014) but, after germination, 7-day-old cotyledons express more distinct 21-nt reads (Zabala et al 2012). …”

Evolutionary Patterns and Coevolutionary Consequences of MIRNA Genes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

“…Overall, miRNA duplicates located in genic regions showed higher levels of abundance than miRNA singletons located in genic regions, but such a difference was rather modest in comparisons between miRNA duplicates and singletons located in unclassified sequences. Because, generally, a small number of miRNAs are predominant in a particular library (Arikit et al, 2014;Zhao et al, 2015), as indicated by the SD of the evaluated expression levels (Table 4), the accumulation levels measured in this set of small RNA data could be somewhat biased. Nevertheless, the distinction was clear for the overall accumulation patterns among the three categories of miRNAs and between the miRNA duplicates and singletons.…”

“…A total of 638 nonredundant MIRNAs (i.e., precursor genes of mature miRNAs) were previously annotated based on small RNA libraries generated from various tissues, including seeds, roots, stems, leaves, flowers, and developing nodules at various stages (Song et al, 2011;Zhai et al, 2011;Arikit et al, 2014;Zhao et al, 2015). However, some of these miRNAs were recently reannotated as siRNA-like miRNAs; thus, the predicted MIRNAs producing these more dubious "miRNAs" were excluded from our analyses.…”

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…The 22-nucleotide miRNAs were reported in legumes to trigger phasiRNA production from more than 74 loci coding for the NB-LRRs (Zhai et al, 2011;Arikit et al, 2014). The resulting phasiRNAs further coregulate en masse, in trans or cis, NB-LRR transcripts.…”