Evolution and genomic organization of muscle microRNAs in fish genomes

BMC Evolutionary Biology

Danillo Pinhal²  Marcos Correa Dias¹  Pedro Gabriel Nachtigall² 

[1] Institute of Health Sciences, UFMT -Federal University of Mato Grosso, Mato Grosso 78550-000, Brazil;Department of Genetics, UNESP - Sao Paulo State University, Institute of Biosciences, Botucatu 18618-970, SP, Brazil

关键词: Paralogs;    Evolution;    Striated muscle;    Comparative genomics;    miRNA;   

Others  :  1117937
DOI  :  10.1186/s12862-014-0196-x

 received in 2014-05-08, accepted in 2014-08-22,  发布年份 2014

【 摘 要 】

Background

MicroRNAs (miRNAs) are small non-coding RNA molecules with an important role upon post-transcriptional regulation. These molecules have been shown essential for several cellular processes in vertebrates, including muscle biology. Many miRNAs were described as exclusively or highly expressed in skeletal and/or cardiac muscle. However, knowledge on the genomic organization and evolution of muscle miRNAs has been unveiled in a reduced number of vertebrates and mostly only reflects their organization in mammals, whereas fish genomes remain largely uncharted. The main goal of this study was to elucidate particular features in the genomic organization and the putative evolutionary history of muscle miRNAs through a genome-wide comparative analysis of cartilaginous and bony fish genomes.

Results

As major outcomes we show that (1) miR-208 was unexpectedly absent in cartilaginous and ray-finned fish genomes whereas it still exist in other vertebrate groups; (2) miR-499 was intergenic in medaka and stickleback conversely to other vertebrates where this miRNA is intronic; (3) the zebrafish genome is the unique harboring two extra paralogous copies of miR-499 and their host gene (Myh7b); (4) a rare deletion event of the intergenic and bicistronic cluster miR-1-1/133a-2 took place only into Tetraodontiformes genomes (pufferfish and spotted green puffer); (5) the zebrafish genome experienced a duplication event of miR-206/-133b; and (6) miR-214 was specifically duplicated in species belonging to superorder Acanthopterygii.

Conclusions

Despite of the aforementioned singularities in fish genomes, large syntenic blocks containing muscle-enriched miRNAs were found to persist, denoting colligated functionality between miRNAs and neighboring genes. Based on the genomic data here obtained, we envisioned a feasible scenario for explaining muscle miRNAs evolution in vertebrates.

【 授权许可】

   
2014 Nachtigall et al.; licensee BioMed Central Ltd.

【 图 表 】

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