Extending the sRNAome of Apple by next-generation sequencing
Date
2014-04
Authors
Visser, Marike
Van der Walt, Anelda P.
Maree, Hans J.
Rees, D. Jasper G.
Burger, Johan T.
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
Abstract
The global importance of apple as a fruit crop necessitates investigations into molecular aspects of the processes that
influence fruit quality and yield, including plant development, fruit ripening and disease resistance. In order to study and
understand biological processes it is essential to recognise the range of molecules, which influence these processes. Small
non-coding RNAs are regulatory agents involved in diverse plant activities, ranging from development to stress response.
The occurrence of these molecules in apple leaves was studied by means of next-generation sequencing. 85 novel
microRNA (miRNA) gene loci were predicted and characterized along with known miRNA loci. Both cis- and trans-natural
antisense transcript pairs were identified. Although the trans-overlapping regions were enriched in small RNA (sRNA)
production, cis-overlaps did not seem to agree. More than 150 phased regions were also identified, and for a small subset of
these, potential miRNAs that could initiate phasing, were revealed. Repeat-associated siRNAs, which are generated from
repetitive genomic regions such as transposons, were also analysed. For this group almost all available repeat sequences,
associated with the apple genome and present in Repbase, were found to produce siRNAs. Results from this study extend
our current knowledge on apple sRNAs and their precursors significantly. A rich molecular resource has been created and is
available to the research community to serve as a baseline for future studies.
Description
Publication of this article was funded by the Stellenbosch University Open Access Fund.
The original publication is available at http://www.plosone.org
The original publication is available at http://www.plosone.org
Keywords
Next-generation sequencing, sRNAome, Fruit crop
Citation
Visser, M., Van der Walt, A.P., Maree, H.J., Rees, D.J.G. & Burger, J.T. 2014. Extending the sRNAome of Apple by next-generation sequencing. PLoS ONE 9(4): doi:10.1371/journal.pone.0095782