Salvelinus fontinalis cDNA
Sequencing a normalized cDNA library to study the effect of natural selection on sequence evolution in the brook charr, Salvelinus fontinalis
The identification of DNA regions evolving under the effect of either positive or stabilizing selection, as well as the quantification of the intensity of the selective pressures at play, represent major challenges in evolutionary biology. While still in its infancy, comparative genomics promises to yield detailed insights into these issues. In non-model species, the combination of next generation sequencing with the comparative genomics approach appears particularly promising towards this end. The main objective of this study was to investigate the patterns of nucleotide substitutions in order to infer the role of natural selection on the evolution of protein coding genes in five species of the salmonid family (Salmo salar, Onchorynchus mykiss, Salvelinus fontinalis, Salvelinus namaycush, Coregonus clupeaformis) in comparison with other fishes (Esox lucius, Danio rerio) for which genome information is available. Our results provided evidence for positive selection at the molecular level across the seven fish genomes that were analysed. More precisely, we i) identified 707 orthologous genes and computed ratio of rates of divergence (dN/dS ratio) to identify those genes that deviated from neutral expectations; ii) associated GO terms to the subset of 72 orthologs found to be under the influence of positive selection and identified 7 biological processes over-represented in this subset of positively selected orthologs, and iii) identified a subset candidates genes that have rapidly evolved under the influence of positive selection within salmonids and warranting further investigation in regards to their putative role in the process of adaptative divergence in salmonids.