TY - JOUR
T1 - Identification of apple miRNAs and their potential role in fire blight resistance
AU - Kaja, Elżbieta
AU - Szcześniak, Michał W.
AU - Jensen, Philip J.
AU - Axtell, Michael J.
AU - McNellis, Timothy
AU - Makałowska, Izabela
N1 - Funding Information:
We thank Penn State Genomics Core Facility, University Park, PA, for performing the sequencing. This project was supported by MPD Programme of Foundation for Polish Science, cofinanced from European Union, Regional Development Fund (Innovative Economy Operational Programme 2007-2013): MPD/2010/3 (IM and EK), by National Science Centre grant no. 2013/09/N/NZ1/01037 (EK), by a scholarship within the project “Scholarship support for Ph.D. students specializing in majors strategic for Wielkopolska’s development,” Sub-measure 8.2.2 Human Capital Operational Programme, co-financed by European Union under the European Social Fund (EK) and by START programme from the Foundation for Polish Science (MS).
Publisher Copyright:
© 2014, The Author(s).
PY - 2015/11/23
Y1 - 2015/11/23
N2 - MicroRNAs (miRNAs) are key players in multiple biological processes; therefore, analysis and characterization of these small regulatory RNAs is a critical step toward a better understanding of animal and plant biology. In apple (Malus domestica), 200 microRNAs are known, which most probably represent only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of 12 small RNA libraries obtained for fire blight-resistant and fire blight-sensitive trees. In the sequencing results, we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop quantitative PCR (qPCR) and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. The gene ontology (GO) enrichment analysis suggests prominent roles of miRNAs in response to stresses, including pathogen infection. In this study, we identified 116 new and confirmed the expression of 143 already known miRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance. The analyses we performed allowed us to define four apple miRNAs potentially involved in fire blight resistance in apple trees: mdm-miR169a, mdm-miR160e, mdm-miR167b-g, and mdm-miR168a,b. These miRNAs are known to be involved in response to stresses across other plant species, usually by targeting stress response proteins. The relatively low number of candidates may result from the high variance of biological replicates and the fact that stress response miRNAs are usually induced by the stress factors and frequently expressed at a low level, or not expressed at all, in normal conditions. The results of our studies are freely available in an online database at http://lemur.amu.edu.pl/share/apple_miRNAs/.
AB - MicroRNAs (miRNAs) are key players in multiple biological processes; therefore, analysis and characterization of these small regulatory RNAs is a critical step toward a better understanding of animal and plant biology. In apple (Malus domestica), 200 microRNAs are known, which most probably represent only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of 12 small RNA libraries obtained for fire blight-resistant and fire blight-sensitive trees. In the sequencing results, we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop quantitative PCR (qPCR) and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. The gene ontology (GO) enrichment analysis suggests prominent roles of miRNAs in response to stresses, including pathogen infection. In this study, we identified 116 new and confirmed the expression of 143 already known miRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance. The analyses we performed allowed us to define four apple miRNAs potentially involved in fire blight resistance in apple trees: mdm-miR169a, mdm-miR160e, mdm-miR167b-g, and mdm-miR168a,b. These miRNAs are known to be involved in response to stresses across other plant species, usually by targeting stress response proteins. The relatively low number of candidates may result from the high variance of biological replicates and the fact that stress response miRNAs are usually induced by the stress factors and frequently expressed at a low level, or not expressed at all, in normal conditions. The results of our studies are freely available in an online database at http://lemur.amu.edu.pl/share/apple_miRNAs/.
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U2 - 10.1007/s11295-014-0812-3
DO - 10.1007/s11295-014-0812-3
M3 - Article
AN - SCOPUS:84919775795
SN - 1614-2942
VL - 11
JO - Tree Genetics and Genomes
JF - Tree Genetics and Genomes
IS - 1
ER -