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. 2019 Dec 31;15(12):907-917.
doi: 10.6026/97320630015907. eCollection 2019.

Analysis of microRNAs and Their Targets From Onion (Allium Cepa) Using Genome Survey Sequences (GSS) and Expressed Sequence Tags (ESTs)

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Free PMC article

Analysis of microRNAs and Their Targets From Onion (Allium Cepa) Using Genome Survey Sequences (GSS) and Expressed Sequence Tags (ESTs)

Rukmini Mishra et al. Bioinformation. .
Free PMC article

Abstract

MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.

Keywords: Allium cepa; ESTs; GSSs; gene ontology; miRNA targets; microRNA.

Figures

Figure 1
Figure 1
Schematic approach for the prediction of miRNAs and their targets from ESTs and GSSs of Allium cepa.
Figure 2
Figure 2
Representative hairpin secondary structures of the predicted onion miRNAs as generated by the MFOLD program. Mature miRNAs are indicated with red lines. (a) ace-miR162, (b) ace-miR168, (c) ace-miR172c, (d) ace-miR172e, (e) ace-miR398, (f) ace-miR400, (g) ace-miR414, (h) ace-miR1134, (i) ace-miR1223, (j) ace-miR6219, (k) ace-miR7725, (l) ace-miR8570, (m) ace-miR8703 and (n) ace-miR8752.
Figure 3
Figure 3
Neighbor-joining phylogenetic tree of the predicted pre-miRNA sequences with their closely related miRNA families from other plant samples. (A) ace-miR172c, (B) ace-miR172e, (C) ace-miR168, (D) ace-miR162 and (E) ace-miR398

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