le hybridization signals phase 3 could represent putative NATs found for the first time in the turbot transcriptome. miRNAs, are one of the most rele vant short NATs classes and function as regulators of gene expression at the level of translation, with an essen tial input in developmental processes. Due to their growing importance in regulating gene expression, several miRNA databases have been already created. In Table 11, we show a selection of ten miRNAs from those identified in the Turbot 3 database including their num ber of reads, which could be considered as a gross indi cator of their expression level. To our knowledge, these miRNAs are the first to be identified in turbot. Further work is being carried out on the turbot database for de veloping a consistent bioinformatic pipeline for miRNA identification, as well as for their validation using a Q PCR approach.

Conclusions This is the first time that the transcriptome of the repro ductive and the immune systems of turbot have been widely explored together. Both systems are essential for the survival of individuals and are of primary importance for commercial aquaculture. This study was designed to fill in the gap of genomic resources in turbot and therefore to improve available turbot sequence databases, specifically in genes related to reproduction. The large amount of gen erated sequences resulted in one of the most complete available databases for flatfish, with more than half of the resources annotated by both gene and functional category.

The detailed and focused se quence assembly and gene annotation strategies allowed the identification of several genes involved in the immune and the reproductive systems, being most of them involved in key functions. A large amount of genetic markers was identified, providing new tools for genomic studies. The performance of an informative pilot microarray was assessed and identification of putative miRNAs was possible. Thus, NGS technologies represent an essential tool to increase exponentially genomic resources in non model species, opening new insights for our understanding Cilengitide of key biological processes and addressing production bottlenecks in their aquaculture. Methods Animals were treated according to the Directive 2010 63 UE of the European Parliament and of the Council of 22 September 2010 on the protection of animals used for experimentation and other scientific purposes.

All experimental protocols were approved by the Institu tional Animal Care and Use Committee of the University of Santiago de Compostela. Sanger sequencing Experimental design and samplings The E. scophthalmi infection trial was performed at the facilities of CETGA. Na ve turbot from a balanced mixture method of five unrelated families with known pedigree, hatched and reared at a commercial fish farm were sent to CETGA facilities and acclimated to experimental condi tions for 10 days before the beginning of the experiment. R and C fish were kept in separate tanks in two separated recircul