Genome-wide profiling of Populus small RNAs

Abstract

BackgroundShort RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.ResultsThe most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).ConclusionsThe short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

“…An intriguing finding from the data presented in Klevebring et al (2009) was that the proposed sexdetermining peritelomeric region of chromosome XIX showed a distinctive pattern of sRNA occurrence that differed significantly from the rest of the genome. Within this region, there was distinct overrepresentation of 21 and 24 nt sRNAs along with a phased siRNA locus.…”

“…In Populus, there are still only a small number of publications that have examined or profiled miRNAs, and only one that has examined the entire sRNA population (Klevebring et al 2009). An intriguing finding from the data presented in Klevebring et al (2009) was that the proposed sexdetermining peritelomeric region of chromosome XIX showed a distinctive pattern of sRNA occurrence that differed significantly from the rest of the genome.…”

“…NBS-LRR genes function in the detection of pathogen occurrence and convey disease resistance signaling to activate gene expression. There is also a disproportionately high occurrence of small (18-24 nt) microRNAs (miRNA) on chromosome XIX coincident to the region containing the putative gender-determining locus and the major cluster of NBS-LRR genes (Klevebring et al 2009). Such miRNAs are a class of posttranscriptional negative regulators that play a vital role in plant development and growth (Jones-Rhoades et al 2006;Shuklaa et al 2008;Henderson et al 2006;Chan et al 2005).…”

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

“…These 2 methods have been used to identify hundreds of miRNAs in several plant species, including the model plant Arabidopsis thaliana (AlvesJunior et al, 2009;Buhtz et al, 2008;Jagadeeswaran et al, 2009;Jin et al, 2008;Klevebring et al, 2009;Song et al, 2009;Sunkar et al, 2005;2008;Szittya et al, 2008;Xie et al, 2007;Zhang et al, 2006b;2007a;2008). Recently, many miRNAs have been shown to regulate a wide range of biological functions of plants.…”

Transcriptome Sequencing

“…Illumina, SOLiD and Helicos technologies are not only clearly better, suited to profiling these small RNAs, they also deliver a greater number of reads. As the read-length of these platforms increases, the ability to generate concatemers of the small RNA-derived cDNA is beneficial, since this can increase the throughput and so allow more samples to be processed and sequenced in parallel (Klevebring et al 2009b).…”