Conifers have a unique small RNA silencing signature

Abstract

Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as RNA silencing. While RNA silencing has been extensively studied across the different phyla of the animal kingdom (e.g., mouse, fly, worm), similar studies in the plant kingdom have focused primarily on angiosperms, thus limiting evolutionary studies of RNA silencing in plants. Here we report on an unexpected phylogenetic difference in the size distribution of small RNAs among the vascular plants. By extracting total RNA from freshly growing shoot tissue, we conducted a survey of small RNAs in 24 vascular plant species. We find that conifers, which radiated from the other seed-bearing plants ;260 million years ago, fail to produce significant amounts of 24-nucleotide (nt) RNAs that are known to guide DNA methylation and heterochromatin formation in angiosperms. Instead, they synthesize a diverse population of small RNAs that are exactly 21-nt long. This finding was confirmed by high-throughput sequencing of the small RNA sequences from a conifer, Pinus contorta. A conifer EST search revealed the presence of a novel Dicer-like (DCL) family, which may be responsible for the observed change in small RNA expression. No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes.

The specific binding to 21-nt double-stranded RNAs is crucial for the anti-silencing activity of Cucumber vein yellowing virus P1b and perturbs endogenous small RNA populations

“…5B). The major peak was at 24 nt in wild-type N. benthamiana plants, as it is usual in angiosperm plant species (Dolgosheina et al 2008), but shifted to 21 nt upon P1b expression. Although this enrichment in 21-nt small RNAs is probably the result of specific P1b binding and consequent stabilization, additional experiments are necessary to rule out possible effects of P1b in enhancing 21-nt small RNA synthesis or 24-nt small RNA degradation, or in repression of the accumulation of the 24-nt species.…”

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

“…1). Picea abies (Norway spruce) lacks 24 nucleotide sRNAs, and it has previously been reported that Pinus contorta also lacks 24 nucleotide siRNAs 19 , which suggests that this is a conserved feature of the Pinaceae family. However, the presence of a strong 24 nucleotide size class in Cycas rumphii, and a small, but still present 24 nucleotide size class in both Ginkgo biloba and in the fern Marsilea quadrifolia suggests that the 24 nucleotide class of sRNAs originated before gymnosperm diversification.…”

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

“…sRNA-seq samples from several non-angiosperm plants lack an immediately obvious signature of abundant 24-nt RNAs, including mosses (Axtell and Bartel, 2005;Arazi et al, 2005), lycophytes You et al, 2017), conifers (Dolgosheina et al, 2008;Montes et al, 2014). These observations led to the suggestion that, unlike phasiRNAs and miRNAs, hc-siRNAs were not universal features found in all land plants (Dolgosheina et al, 2008).…”

“…These observations led to the suggestion that, unlike phasiRNAs and miRNAs, hc-siRNAs were not universal features found in all land plants (Dolgosheina et al, 2008). However, homologs of key genes known to be responsible for hcsiRNA biogenesis and function in angiosperms clearly exist in diverse plant lineages (Zong et al, 2009;Banks et al, 2011;Huang et al, 2015;Wang and Ma, 2015;You et al, 2017).…”