The evolution of flatfish (order Pleuronectiformes) towards a sea-bottom lifestyle has involved sharp morphological changes , such as the acquisition of a flattened shape ("flatfish") and the characteristic bilateral asymmetry. Pleuronectiformes is a highly diverse polyphyletic group resulting from a quick adaptive radiation (around 700 species) , dated back to the Pliocene (~70 MYA), and which has adapted to a wide variety of benthonic environments (Lü et al. , 2022). Flatfish have evolved into compact genomes (500-700 Mb) with a low proportion of repetitive DNA elements (< 8%), which has facilitated assembly and annotation, so currently, Pleuronectiformes are among the fish with most confident and wide genomic resources (Robledo et al., 2017).
The particular environmental characteristics of the sea-bottom, like the low light radiation and low temperature , needs from specific adaptations to enhance vision (green light) , as well as enhancement of alternative sensory systems, such as the olfactory system, as it has been hypothesized (Figueras et al., 2016) . The e arly development of olfactory organs in fish underscores the essential role of the sense of smell in their interactions with conspecifics and the environment. In order to investigate the evolutionary history of the genes related to olfaction and better understand the evolution of the olfactory system in this group, we performed a comparative genomics study on some relevant flatfish species with chromosome-level assembly and well-annotated genomes pertaining to 5 different families : Solea senegalensis (Soleidae) , Hippoglossus hippoglossus , Reinhardtius hippoglossoides, Verasper variegatus (Pleuronectidae), Scophthalmus maximus (Scophthalmidae) , and Cynoglossus semilaevis (Cynoglossidae ) using two bilateral and pelagic related teleosts as outgroups : Oryzias latipes and Danio rerio. We aim at identifying contractions or expansions in olfaction-related genes that could be eventually associated to specific evolutionary pressures , thus providing new insights into the role of olfaction in the adaptation these unique fish in their habitats . Additionally, our analyse s have focused specifically on the Senegalese sole, an emerging aquaculture species in Europe that still faces challenges in captive reproduction, where chemical communication mediated by the olfactory system might be involved .
Material and Methods
The transcriptomes were downloaded from Ensembl . The longest protein for each gene was selected using a custom Python script. Orthology relationships were determined using OrthoFinder (Emms & Kelly, 2019). Phylogenetic relationships were represented using FigTree v1.4.4.
A total of 184,534 genes from the 8 species were grouped into 20,151 orthogroups , of which 7,074 are single-copy orthogroups, and therefore represent single-copy genes across the whole teleost phylogeny. The species tree placed zebrafish and medaka as sister branches out of the Pleuronectiformes cluster, consistent with the teleost phylogeny (Figure 1A). Further, grouping of families in the order was also consistent with previous reports . We did not observe a common evolutionary trend in olfaction-related genes in flatfish, suggesting species-specific adaptations of the olfactory system. Nevertheless, some expansions in genes related with sensory perception were detected . Particularly, the Senegalese sole showed a high number of genes in some orthogroups related to sensory perception through olfaction unlike the remaining species of the order (Figure 1B). Additional analyses are required to further investigate the evolutionary patterns of olfactory genes in flatfish and to better understand the species-specific adaptations of the olfactory system. Furthermore, the role of the olfactory system in reproduction, as an essential aquaculture trait, should be explored.
Lü, Z., Gong, L., Ren, Y., Chen, Y., ... & Li, Y. (2021). Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan. Nature Genetics , 53(5), 742-751.
Robledo, D., Martin, A. P., Álvarez‐Dios, J. A., Bouza, C., & Martínez, P. (2017). First characterization and validation of turbot microRNAs. Aquaculture , 472, 76-83.
Figueras, A., Robledo, D., Corvelo , A., Hermida, M., Pereiro, P., Rubiolo, J. A., ... & Martínez, P. (2016). Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes ): a fish adapted to demersal life. DNA research , 23(3), 181-192.
Emms , D. M., & Kelly, S. (2019). OrthoFinder : phylogenetic orthology inference for comparative genomics. Genome biology , 20, 1-14.