Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

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.

Transcriptomic analysis to reveal the differentially expressed miRNA targets and their miRNAs in response to Ralstonia solanacearum in ginger species

“…In ginger it targets mainly FRS6. miR1223 was reported previously in Allium cepa [57] and Physcomitrella patens [58]. This miRNA upregulated in the rhizome of both ginger and mango ginger, till 12 h post-infection (Fig.…”

Unravelling the Differential Expression of Potential microRNAs in Bacterial Wilt-resistant and Susceptible Ginger Species

“…It targets mainly nucleic acid binding and secondary metabolic process. miR1223, was reported previously in Allium cepa 52 and Physcomitrella patens 53 . Ppt-miR1223 was found to upregulate in rhizome of both ginger and mango ginger till 12 h post infection.…”

The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba

“…Among the core miRNAs, aly-miR157d-3p and pta-miR319 were identified in comparison to SS1, and aly-miR157d-3p was simultaneously identified in the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks. aly-miR172e-3p is also a potential miRNA that might regulate transcription factors implicated in plant growth [28]. There are limited reports of miR395b and miR6300 relevant to plant growth within the scope of existing research [29].…”