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Open Access Research

Apple miRNAs and tasiRNAs with novel regulatory networks

Rui Xia123, Hong Zhu23, Yong-qiang An4, Eric P Beers2 and Zongrang Liu23*

Author Affiliations

1 Alson H Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, VA 22602, USA

2 Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA

3 Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV 25430, USA

4 Plant Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Donald Danforth Plant Science Center, St Louis, MO 63132, USA

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Genome Biology 2012, 13:R47  doi:10.1186/gb-2012-13-6-r47

Published: 15 June 2012

Abstract

Background

MicroRNAs (miRNAs) and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown.

Results

We performed deep small RNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that 10 of the 19 miR828-targeted MYBs undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis.

Conclusions

Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family.