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Updated: May 4, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Differentially-expressed opsin genes identified in Sinocyclocheilus cavefish endemic to China
Fanwei Meng1, Yahui Zhao1, John H Postlethwait2
1Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Abstract:
Eye degeneration is a common troglomorphic character of cave-dwelling organisms. Comparing the morphology and molecular biology of cave species and their close surface relatives is a powerful tool for studying regressive eye evolution and other adaptive phenotypes. We compared two co-occurring and closely-related species of the fish genus Sinocyclocheilus, which is endemic to China and includes both surface- and cave-dwelling species. Sinocyclocheilus tileihornes, a cave species, had smaller eyes than Sinocyclocheilus angustiporus, a surface species. Histological and immunohistochemical analyses revealed that the cavefish had shorter cones and more disorderly rods than did the surface-dwelling species. Using quantitative PCR and in situ hybridization, we found that rhodopsin and a long-wavelength sensitive opsin had significantly lower expression levels in the cavefish. Furthermore, one of two short-wavelength-sensitive opsins was expressed at significantly higher levels in the cavefish. Changes in the expression of opsin genes may have played a role in the degeneration of cavefish eyes.
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