TY  - JOUR
AU  - Arias-Pérez, Alberto
AU  - Ramírez-Torres, Daniel
AU  - Rodríguez, María E.
AU  - Portela-Bens, Silvia
AU  - García-Suarez, Emilio
AU  - Merlo, Manuel A.
AU  - García-Angulo, Aglaya
AU  - Cross, Ismael
AU  - Rebordinos, Laureana
AU  - Liehr, Thomas
PY  - 2018
DA  - 2018/10/24
TI  - In Silico Detection and FISH Analysis to Determine Location of miRNAs in <i>Solea senegalensis</i> Chromosomes Using BACs
JO  - OBM Genetics
SP  - 044
VL  - 02
IS  - 04
AB  - Background: MicroRNAs (miRNAs) are small, non-coding RNAs that play a very important role in gene expression by regulating mRNA cleavage and translation. The Senegalese sole, Solea senegalensis (Kaup 1858), is a flatfish species that shows great potential for marine aquaculture. Nevertheless, the existence of sexual dysfunction of males reared in captivity, high larval mortality, and diseases have hampered its production. The integration of sequence information with data on chromosomal physical location is useful for understanding genetic processes and is essential for comparative analysis, quantitative trait locus (QTL) mapping, and positional cloning of genes. Methods: In this study we employed an in silico approach to identify potential miRNAs in an S. senegalensis BAC library. Mature sequences were obtained from miRBase and other sources, and a BLAST analysis was carried out against sequences from an S. senegalensis BAC library. Sequences showing similarity were extracted and subjected to analysis of their secondary structure. This information was combined with BAC-FISH data to assign miRNAs to particular chromosomes. In addition, a phylogenetic analysis of some miRNA families was carried out and target genes were predicted against a reference transcriptome. Results: After secondary structure analysis, 45 groups of sequences showed similarity to mature miRNAs. Of these, 19 were assigned to Senegalese Sole chromosomes using BAC-FISH data, and 34 unique mature sequences targeted 12387 sequences from an S. senegalensis reference transcriptome. Phylogenetic trees showed different levels of support for clustering among types of miRNAs; S. senegalensis sequences were usually close to those of other Pleuronectiformes. Conclusions: These results will be helpful for understanding how miRNAs affect gene expression in this species and the biological processes involved in its aquaculture. Nevertheless, experimental validation using RT-PCR, northern blotting, or microarrays, is required to confirm the predictions made here.
SN  - 2577-5790
UR  - https://doi.org/10.21926/obm.genet.1804044
DO  - 10.21926/obm.genet.1804044
ID  - Arias-Pérez2018
ER  -