Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia.
Using a combined computational program, we identified 50 potential microRNAs (miRNAs) in Giardia lamblia, one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs, currently known in other species, were not found in G. lamblia. This suggests that miRNA biogenesis and miRNA-mediated gene regulation pathway may evolve independently, especially in evolutionarily distant lineages. A majority (43) of the predicted miRNAs are located at one single locus; however, some miRNAs have two or more copies in the genome. Among the 58 miRNA genes, 28 are located in the intergenic regions whereas 30 are present in the anti-sense strands of the protein-coding sequences. Five predicted miRNAs are expressed in G. lamblia trophozoite cells evidenced by expressed sequence tags or RT-PCR. Thirty-seven identified miRNAs may target 50 protein-coding genes, including seven variant-specific surface proteins (VSPs). Our findings provide a clue that miRNA-mediated gene regulation may exist in the early stage of eukaryotic evolution, suggesting that it is an important regulation system ubiquitous in eukaryotes.
Zhang
Yan-Qiong
YQ
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Chen
Dong-Liang
DL
Tian
Hai-Feng
HF
Zhang
Bao-Hong
BH
Wen
Jian-Fan
JF
D019295:Computational Biology; D003198:Computer Simulation; D030541:Databases, Genetic; D016678:Genome; D016829:Giardia lamblia / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008957:Models, Genetic
D035683:MicroRNAs