We are focused on the creation of genomic resources in non-model species for the optimal development of subsequent studies.
We are currently working on several projects focused on non-model species (species without an available reference genome). The lack of genetic resources in these species has led us to work on an initial step of discovery and validation of genomic markers for them, thereby creating in a parallel manner, a new research line.
We have moved from using conventional cloning and Sanger sequencing techniques to specializing in the application of new technologies of massive sequencing or Next Generation Sequencing (NGS) with different objectives: the construction of reference genomes and transcriptomes by means of de novo assembly, the annotation and functional prediction of genes, and the detection of DNA variants for the design of panels of markers such as SNPs, indels (short insertions and deletions) or CNVs. In addition, we have also included in our work strategy RAD-seq (Restriction-site associated DNA sequencing) and GBS (Genotyping By Sequencing) where NGS technologies are applied to genome Reduced Representation Libraries (RRLs).
To date, and using Illumina Hiseq and Roche 454 sequencing platforms, we have worked on the assembly and description of the variability of the genomes and transcriptosomes of the following species:
- European anchovy (Engraulis encrasicolus)
- Atlantic bluefin tuna (Thunnus thynnus)
- clam (Ruditapes philippinarum)
- Atlantic mackerel (Scomber scombrus)
We also work towards the creation of bioinformatics tools which facilitate the achieving of our objectives. Recently, for example, we have developed a pipeline for the identification of SNPs from reference transcriptosomes constructed by our group, which takes into account existing intron/exon boundaries in order to improve the SNP genotyping conversion rate.