Researchers from Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai Ocean University and other institutes have successfully decoded the genome of a flatfish -- Japanese flounder (Paralichthys olivaceus), combing another flatfish (Cynoglossus semilaevis) genome to provide insights into the extraordinary asymmetrical specialization of flatfish. The latest study has been published online recently in Nature Genetics (doi:10.1038/ng.3732).

Flatfish metamorphosis is one of the most extraordinary anatomical specializations including the eye migration, the asymmetrical pigmentation, the extensive craniofacial remodeling, the muscle thickness asymmetry, which determine the switch from a pelagic to a benthic lifestyle. The evolutionary origin of this metamorphosis was recently documented but the biological basis still remains an enigma even though the obligatory role of thyroid hormones (THs) was identified in the early 1980’s. In this study, the scientist hypothesized that the basis of the unique specialization in flatfish should be apparent in the genome and detectable in the transcriptome since TH receptors are ligand activated transcription factors. They thus generated a high quality reference genome (546 Mb) of the Japanese flounder, which shared extensive conserved synteny (86.2%) with the Chinese tongue sole. Through comparative genomics of two distantly related flatfish, one hundred and fifty-three gene families were specific for the flatfish lineage and 12 flatfish specific gene family expansions and 106 positively selected genes were identified. Comparative transcriptome analyses during symmetry to asymmetry generation identified 2,307 differentially expressed protein-coding orthologs for both species and included positively selected genes of the TH system and retinoic acid system. TH signaling was asymmetric in the skull, together with genes of the RA system that generates the left-right asymmetric RA gradient necessary for eye migration and asymmetric pigmentation in Japanese flounder. They anticipate that the opsin genes (rh1, rh2, lws, sws1 and sws2) of the phototransduction pathway with an unexpected expression in skin act as the translators of illumination differences that generate the RA-gradients that underpin asymmetry generation.

Understanding these unique asymmetry mechanisms not only answers a Darwinian evolutionary debate, it may also accelerate the genetic breeding procedure of Japanese flounder and benefit flatfish aquaculture.