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Genome-wide profiling of Populus small RNAs

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https://ir.library.oregonstate.edu/concern/articles/h989r3980

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  • Background: Short 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. Results: The 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). Conclusions: The 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.
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  • Klevebring, D., Street, N. R., Fahlgren, N., Kasschau, K. D., Carrington, J. C., Lundeberg, J., Jansson, S. (2009). Genome-wide profiling of populus small RNAs. BMC Genomics, 10(620)
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  • 10
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  • The authors wish to thank Kicki Holmberg, Christian Nathanaelsson and Annika Åberg for help with preparation prior to 454 sequencing. We also thank Anna Westring for her kind help with graphical issues and Dr. Magnus Bjursell, Dr. Johan Lindberg and Dr. Andreas Sjödin for bioinformatics support, provision of analysis scripts and informative discussion. This work was supported by Swedish Research Council and Knut and Alice Wallenberg Foundation
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