Genome-wide proﬁling of Populus small RNAs
2009 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 10, Article number 620- p.Article in journal (Refereed) Published
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 and these were generally associated with a number of classes of retrotransposons and repetitive elements. Some repetitive elements were also associated with 22 nt RNAs. We identiﬁed an sRNA hot-spot on chromosome 19, overlapping a region containing both the sex-determining loci 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. 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. 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, Article number 620- p.
stress-responsive micrornas; dna-methylation; arabidopsis-thaliana; sirna biogenesis; repetitive elements; mirna genes; trichocarpa; plants; database; expression
Other Biological Topics
IdentifiersURN: urn:nbn:se:kth:diva-11443DOI: 10.1186/1471-2164-10-620ISI: 000273971100001ScopusID: 2-s2.0-75449114906OAI: oai:DiVA.org:kth-11443DiVA: diva2:276124
QC 201007232009-11-102009-11-102010-12-06Bibliographically approved