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

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.

In silico analysis of onion chitinases using transcriptome data.

Chitinases are glycoside hydrolase (GH) family of proteins having multifaceted roles in plants. It is of interest to identify and characterize chitinase-encoding genes from the popular bulbous plant onion (Allium cepa L.). We have used the EST sequences for onion chitinases to elucidate its functional features using sequence, structure and functional analysis. These contigs belong to the GH19 chitinases family according to domain architecture analysis. They have highly conserved chitinase motifs including motifs exclusive to plant chitinases as implied using the MEME based structural characterization. Estimation of biochemical properties suggested that these proteins have features to form stable and hydrophilic proteins capable of localizing extracellular and in vacuoles. Further, they have multiple cellular processes including defense role as inferred by DeepGO function prediction. Phylogenetic analysis grouped them as class I and class VII plant chitinase, with possible abundance of class I chitinase in onion. These observations help in the isolation and functional validation of onion chitinases.