Parallel evolution of LRP2 gene mediating telescope-eye and celestial-eye in goldfish

After the intensive artificial selection, the development of celestial-eye in goldfish involves the protuberating and turning upwards of eyeballs, and also degeneration of the retinal. Thus, the celestial-eye goldfish provides an excellent model for both evolutionary and human ocular disease studies. Here, two mapping populations with segregating eye phenotypes in the offspring goldfish were constructed. Though whole genome sequencing using individual samples from the parents and pooled samples from the offspring, and RNA-seq for eyeball samples from pure goldfish lines, a premature stop codon in Exon 38 of LRP2 gene was identified as the top candidate mutation that is responsible for celestial-eye in goldfish. Fatty acid metabolisms and epidermal cells, especially keratocytes related functions were inhibited in the eyeballs of celestial-eye, while inflammatory reactions and extracellular matrix secreting were stimulated. These suggest the dysfunction of cornea in the celestial-eye, and same for retinal, which could be the results of the truncated LRP2 protein. Besides, evidence was provided that not all the goldfish lines share the same causal mutation for celestial-eye, while the same gene LRP2 is in charge of the similar phenotypes (celestial-eye and telescope-eye) in goldfish but no shared mutation. Therefore, those mutations and the associated phenotypes exhibit parallel evolutions in molecular level under artificial selections. Overall, the candidate mutation for celestial-eye in goldfish was identified by this study, and further analyses provide insights into the developmental and evolutionary processes of morphological changes in the eyes of goldfish. Author SummaryAs the first domesticated ornamental fish, goldfish is now worldwide spread and has undergone intensively artificial selections for morphological variations. Among them, celestial-eye is one of the most unique traits for goldfish, which consists of enlarged and protuberant eyes while the eyeballs turning upwards and thus suitable for top viewing in pots. In this study, we have identified that a single nucleotide mutation resulting in disrupted function of LRP2 gene, is responsible for the celestial-eye phenotype. Together with our transcriptome analysis, the genetic and cellular mechanisms for celestial-eye in goldfish were reported for the first time, which provides fundamental knowledge for further studies about the development of eyes in fish and also for ophthalmic diseases in humans. In the aspect of evolution, our study and previous studies reported different truncated LRP2 proteins in charge of celestial-eye and telescope-eye, respectively, which are excellent materials to understand the mechanisms of parallel evolution in molecular level, i.e., independent artificial selections resulting in mutations of the same gene.