Background: MicroRNAs (miRNAs) are endogenous small non-coding
RNAs with 18-24 nucleotides in length, which have important roles in posttranscriptional
gene regulation. The resemblance of miRNA biogenesis in unicellular
green algae and those in plants suggests probable evolutionary conserved pathways.
This conservation provides a ground towards prediction of new homologs via computational
Methods: Here, conserved miRNA genes in Chlamydomonas reinhardtii and plants
were examined through homology alignment. Previously known and unique plant
miRNAs were BLASTed against expressed sequence tags (ESTs) and genomic survey
sequences (GSSs) of C. reinhardtii. All candidate sequences with appropriate
fold back structures were screened according to a series of miRNA filtering criteria.
Results: Homologous miRNAs (17), belonging to 9 miRNA gene families were predicted. Interestingly
and for the first time, a miRNA family of genes was localized to chloroplast. Again and for the first
time, here we report identification of C. reinhardtii miRNA orthologs in plants and animals. miRNA
target genes were identified based on their sequence complementarities to the respective miRNAs using
psRNATarget against C. reinhardtii, Unigene, and DFCI Gene Index (CHRGI). Totally, 152 potential
target sites were identified. From the predicted miRNAs, 7 miRNAs had no target sequence in C. reinhardtii
protein coding genes.
Conclusion: Identifying miRNA and their target transcript(s) would be useful for other research concerned
with the function and regulatory mechanisms of C. reinhardtii miRNAs and helps researchers to
better understand the nature of its extensive metabolic flexibility and environmental compatibility to
survive in distinct environmental niches and nutrient availability.