Pigmentation patterns in Rajidae (class Chondrichthyes): the genetic basis of spots revealed by transcriptome analysis

Animal patterning has always been investigated as one of the possible drivers involved in the enigmatic mechanism of speciation. However, the molecular basis of skin pigmentation and its adaptive meaning are still poorly investigated. Therefore, this topic is one of the most intriguing among Evolutionary biologists. Skates are bottom dwelling cartilaginous fishes inhabiting worldwide oceans and whose phylogeographic structures were widely influenced by hydro-geographical isolation resulting from paleo-climatological events. Some recently diverged species show a strikingly stable external morphology and particular dorsal patterning 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 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 showing a convergent pigmentation and strong monophyly (the Mediterranean R. miraletus and the South African R. ocellifera). We then assembled a reference transcriptome of R. miraletus based on Ion Torrent NGS. 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