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Genome-wide profiling of populus small RNAs
School of Biotechnology, Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, 106 91 Stockholm, Sweden.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0001-6031-005X
Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA.
Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA.
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2009 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 10, 620- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2009. Vol. 10, 620- p.
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Biological Sciences
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URN: urn:nbn:se:umu:diva-31867DOI: 10.1186/1471-2164-10-620PubMedID: 20021695OAI: oai:DiVA.org:umu-31867DiVA: diva2:297962
Available from: 2010-02-19 Created: 2010-02-19 Last updated: 2017-12-12Bibliographically approved

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