Apple miRNAs and tasiRNAs with novel regulatory networks.
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.
Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Rui
R
Xia
Hong
H
Zhu
Yong-Qiang
YQ
An
Eric P
EP
Beers
Zongrang
Z
Liu
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D027845:Malus / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D017423:Sequence Analysis, RNA / Q000379:methods; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D035683:MicroRNAs; C500589:Myb protein, Arabidopsis; D018749:RNA, Plant; D034741:RNA, Small Interfering; D014157:Transcription Factors