Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

Abstract

In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.

Resolving Cypriniformes relationships using an anchored enrichment approach

“…By comparing the genome of the Zebra Danio with close relatives, the role of mutations and gene expression can be determined. Comparative genomic studies within Cypriniformes have already benefited from the foundation and annotation of the Zebra Danio genome sequence to generate insights into the functional evolution of various adaptations including adaptation to harsh environments such as caves and high altitude streams [82, 83]. With a robust phylogeny, we can get a much better understanding of the function of genes by treating relatives of the Zebra Danio as natural mutants screened by natural selection [1].…”

Complete mitochondrial genome of a cavefishSinocyclocheilus ronganensis(Cypriniformes: Cyprinidae)

“…Sinocyclocheilus ronganensis, a cavefish and is newly found in the karst river of Rong'an county, Southwestern China (Luo et al 2016). Like other surface-dwelling species (Zhao & Zhang 2009;Meng et al 2013), S. ronganensis has normal eyes, full-cover scales but larger than most of them, and it is a good model for studying the genetic status and evolutionary by comparing the mitochondrial genome.…”

Cavefish and the basis for eye loss

“…When studying the adult forms of one cavefish species of this genus (S. anophthalmus), it was discovered that they possess regressed eyes similarly buried under the skin as they are in Astyananx, but the overall eye structure remained intact. The authors reported fully formed lenses, cornea, iris and retinal structures, even though the retina was notably thinner than in surface fish [6,69].…”