Journal Article
Comparative transcriptome profiling of the loaches Triplophysa bleekeri and Triplophysa rosa reveals potential mechanisms of eye degeneration
Zhao, Q., Zhang, R., Xiao, Y., Niu, Y., Shao, F., Li, Y. and Peng, Z.
Record Number:
4530
Year:
2020
Journal:
Frontiers in Genetics
Volume:
10:1334
Abstract:
Eye degeneration is one of the most obvious characteristics of organisms restricted to
subterranean habitats. In cavefish, eye degeneration has evolved independently
numerous times and each process is associated with different genetic mechanisms. To
gain a better understanding of these mechanisms, we compared the eyes of adult
individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri.
Compared with the normal eyes of the surface loach, those of the cave loach were found
to possess a small abnormal lens and a defective retina containing photoreceptor cells
that lack outer segments. Sequencing of the transcriptomes of both species to identify
differentially expressed genes (DEGs) and genes under positive selection revealed 4,802
DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we
identified one Gene Ontology category related to vision that was significantly enriched in
downregulated genes. Specifically, we found that many of the downregulated genes,
including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and b|g-crystallin are associated with
lens/retinal development and maintenance. However, compared with those in the surface
loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa
indicate that changes in amino acid sequences might be involved in the adaptation and
visual degeneration of cave loaches. We also found that genes associated with light
perception and light-stimulated vision have evolved at higher rates (some genes dN/dS >
1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of
cavefish vision is probably associated with both gene expression and amino acid changes
and provide new insights into the mechanisms underlying the degeneration of
cavefish eyes.
Keywords: cavefish, Triplophysa rosa, transcriptome, eye degeneration, lens, photoreceptor
Times Cited:
1
Relevent Species:
Related Records:
Wu, He and Li (2005)
Linemacheilus wulong
Chen, X.Y. and Yang, J. (2005)Triplophysa rosa sp. nov.: A new blind loach from China
Wu, Q., He, L.J., Zhen, S.M. and Li, L.G. (2007)White bubble blind fish - Wulong Li rod-shaped loach Heminoemacheilus wulongensis
Wang, J.J., Tang, Q.Y., Wang, Z.J., Zhang, Y.G., Wu, Q. and Peng, Z.G. (2012)The complete mitogenome sequence of a cave loach Triplophysa rosa (Telestei, Balitoridae, Nemacheilinae)
Kottelat, M. (2012)Draconectes narinosus, a new genus and species of cave fish from an island of Halong Bay, Vietnam (Teleostei: Nemacheilidae).
Huang, J. (2012)Comparative studies on the gross anatomy and histological structure of the central nervous system between. In: Triplophysa bleekeri and Triplophysa rosa
Zhao, J., Zhao, K. and Peng, Z. (2014)Development and characterization of eleven microsatellite markers for an endangered cavefish (Triplophysa rosa Chen and Yang, 2005) using 454 sequencing
Wang, Y., Shen, Y., Feng, C., Zhao, K., Song, Z., Zhang, Y., Yang, L. and He, S. (2016)Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Niu, Y., Zhao, Q., Zhao, H., Ludwig, A. and Peng, Z. (2016)Karyotype and genome size of an endangered cavefish (Triplophysa rosa Chen & Yang, 2005)
Li, J.X. Wang, Y., Jina H.F.,Li, W.J., Yan, C.C., Yan, P.F., Zhang, X.Y., He, S.P. and Song, Z.B. (2017)Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes
Liu, S., Ludwig, A. and Peng, Z. (2017)Nine novel microsatellites for the cavefish (Triplophysa rosa Chen)
Niu, Y. (2017)Comparative histological study of visual organs between Triplophysa rosa and Triplophysa bleekeri
Xiao, Y. (2017)Genetic basis of the albinism in the cavefish Triplophysa rosa
Zhang, Y., Wang, Z., Zhang, Z., Wu, M.. Chen, J. and Zhao, Y. (2018)The complete mitochondrial genome of Triplophysa brevibarba with phylogenetic consideration
Shi, C., Yao, M., Lv, X., Zhao, Q., Peng, Z. and Luo, Y. (2018)Body and organ metabolic rates of a cave fish, Triplophysa rosa: influence of light and ontogenetic variation
Wu, W.J., He, A.Y., Yang, J.X. and Du, L.N. (2018)Description of a new species of Triplophysa (Teleostei: Nemacheilidae) from Guizhou Province, China
Sgouros, K., Page, L.M., Orlofske, S.A. and Jadin, R.C. (2019)A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)
Yang, X., Liu, H., Ma, Z., Zou, Y., Zou, M., Mao, Y., Li, X., Wang, H., Chen, T.,Wang, W. and Yang, R. (2019)Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau
Huang, T.F., Zhang, P.L., Huang, X.L., Wu, T., Gong, X.Y., Zhang, Y.X., Peng, Q.Z. and Liu, Z.X. (2019)A new cave-dwelling blind loach, Triplophysa erythraea sp. nov. (Cypriniformes: Nemacheilidae), from Hunan Province, China.
Zhao, Q., Zhang, R., Xiao, Y., Niu, Y., Shao, F., Li, Y. and Peng, Z. (2020)Comparative transcriptome profiling of the loaches Triplophysa bleekeri
and Triplophysa rosa reveals potential mechanisms of eye degeneration
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Xu, Y., Jing, Y., Zhou, J., Long, R., Meng, J. Yang, Y. and Luo, Y. (2023)Age, growth, and energy storage of the cavefish Triplophysa rosa
Xu, Y., Jing, Y., Zhou, J., Long, R., Meng, J. Yang, Y. and Luo, Y. (2023)Age, growth, and energy storage of the subterranean fish Triplophysa rosa (Cypriniformes: Nemacheilidae) from Chongqing, China
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Wang, Y.D., Dong, X.Y. and Liu, H.B. (2024)The complete mitochondrial genome of Triplophysa erythraea (Huang et al. 2019)(Cypriniformes, Nemacheilidae)