The genetic basis of eyespot pigmentation patterns in Rajidae (subclass Elasmobranchii) revealed by next-generation transcriptome sequencing

Animal pigmentation has always been one of the most fascinating topics for Evolutionary Biologists, since for some species it can be considered one of the drivers involved in the mysterious mechanism of speciation. However, the molecular underpinnings of most pigmentation patterns and their adaptive meaning are still poorly investigated or focusing on a small share of the biodiversity we can admire. Skates (family Rajidae) are cartilaginous fishes inhabiting the continental shelf and slope of worldwide oceans and they typically show strong phylogeographic structures, which has been attributed to hydro-geographical isolation resulting from paleo-climatological events. Some recently diverged species are characterised by stable gross morphology and particular dorsal patterning (e.g. in the form of colourful eyespots) which could have been implicated with cryptic speciation events. In order to investigate the genetic basis of eyespots in skates, we performed transcriptomic profiling of different skin tissues from five nominal species. More specifically, we first assembled a reference transcriptome of R. miraletus based on Ion Torrent next-generation sequencing. We then conducted Illumina based RNA-sequencing of different skin pattern motifs of (i) recently diverged species in comparison to their sibling species (Raja clavata, R. straeleni and R. asterias respectively) and (ii) species that show a convergent pigmentation and strong monophyly (the Mediterranean R. miraletus and the South African R. ocellifera). This enabled us to quantify differential gene expression between species and eyespot patterns. Our results provide the basis for examining the connection between pigmentation patterns in skates and their diversification.