Computational Identification, Characterization and Analysis of Conserved miRNAs and their Targets in Amborella Trichopoda

MicroRNAs (miRNAs) are single stranded non-coding endogenous small RNAs of about 22 nucleotides, which are directly involved in regulating gene expression at post transcriptional level. miRNAs play key roles in development and response to biotic and abiotic stresses. Homology searches allow identification of new miRNAs due to their relative high conservation in plant species. Here, miRNAs were identified for Amborella trichopoda. Known and unique plant miRNAs from miRBase were BLAST-searched against Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS) in A. trichopoda. All candidate sequences with appropriate fold back structures were screened by a series of miRNA filtering criteria. Finally, we identified and analysed conservation of 5 potential conserved miRNAs belonging to 5 miRNA gene families from ESTs as well as 82 newly identified miRNAs belonging to 39 miRNA families from GSSs. Potential target genes of identified miRNAs were identified based on their sequence complementarities to the respective miRNAs using psRNATarget against scaffold assignment of A. trichopoda genome sequences. Totally, 1219 target sites in A. trichopoda genome were identified. From which, 941 (77.19%) were predicted to be the subject of miRNA cleavage and 278 (22.81%) scaffolds were regulated via translational repression of mRNA. From the predicted miRNAs, 18 had no target sequence in A.trichopoda.