Computational identification and functional annotation of microRNAs and their targets in three species of kiwifruit (Actinidia spp.)
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MicroRNAs (miRNAs) are a class of small non-coding RNA of approximately 22 nucleotides in length derived from one arm of hairpin stem-loop secondary precursors, that regulates gene expression at the transcriptional or post-transcriptional level either through cleavage or translation inhibition of the target mRNA. In the present study, an attempt was made to identify conserved miRNAs in Actinidia delicosa, Actinidia chinensis, and Actinidia eriantha expressed sequence tags (ESTs) through computational approach. To identify the novel miRNAs, 57757 ESTs of A. delicosa, 47384 ESTs of A. chinensis and 12650 EST sequences of A. eriantha were analysed. A total of 16 miRNAs from A. chinensis, 3 from A. eriantha and 1 from A. delicosa were predicted with their pre-miRNAs forming a stem-loop structure. psRNATarget server identified a total of 75 target genes including transcription factors, kinases, binding proteins, transporters that were involved in flower development, sucrose biosynthesis, stress responses. The results from the present study will shed more light on understanding the functions of miRNA in regulating the growth and development of Actinidia spp.
KeywordsmiRNA ESTs kiwifruit mfold psRNAtarget
KJD, PS, SC, and RR acknowledge Assam University, Silchar, Assam, India for providing infrastructural facility to carry out the present study. KJD acknowledges University Grants Commission (India) for non-NET fellowship. RR acknowledges funding from Department of Science & Technology (DST), Science & Engineering Research Board (SERB), Government of India vide grant no. EEQ/2016/000501.
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Conflict of interest
The authors declare that they have no conflicts of interest.
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