Journal Article
First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J.
Record Number:
5208
Year:
2021
Journal:
Research Square Preprint
Notes:
This preprint is under consideration at BMC Ecology and Evolution
Abstract:
Background
Loaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling
freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species
contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle,
facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwellingrelated
traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study
objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for
research into the evolution of cavefishes.
Results
Here we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated
approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing.
Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately
515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 proteincoding
genes were predicted, of which 95.65% have been functionally annotated. We also performed genome resequencing
of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID
showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type
eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling
Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O.
daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.
Conclusions
We here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for
Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for
loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to
the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).
Times Cited:
4
Relevent Species:
Related Records:
Zheng, J.Z. (1981)
Oreonectes anophthalmus
Zhao, Z. (1983)New discovery of cave blind fish in Wuming, Guangxi
Zhou, J. (1985)Fishes in karst caves of Guangxi
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Yue, P. and Chen, Y. (1998)China Red Data Book of Endangered Animals. Pisces
Yang, J., Wu, T.J., Wei, R.F. and Yang, J. (2011)A new loach, Oreonectes luochengensis sp. nov. (Cypriniformes: Balitoridae) from Guangxi, China.
Kottelat, M. (2012)Conspectus cobitidum: An inventory of the loaches of the world (Teleostei: Cypriniformes: Cobitoidei)
Kottelat, M. (2012)Conspectus cobitidum: An inventory of the loaches of the world (Teleostei: Cypriniformes: Cobitoidei)
Lan, J.H., Gan, X., Wu, T.J. and Yang, J. (2013)Cave fishes of Guangxi, China
Lan, J.H., Gan, X., Wu, T.J. and Yang, J. (2013)Cave fishes of Guangxi, China
Fenolio, D.B., Zhao, Y., Niemiller, M.L. and Stout, J.F. (2013)In-situ observations of seven enigmatic cave loaches and one cave barbel from Guangxi, China, with notes on conservation status
Fenolio, D.B., Zhao, Y., Niemiller, M.L. and Stout, J.F. (2013)In-situ observations of seven enigmatic cave loaches and one cave barbel from Guangxi, China, with notes on conservation status
Waryani. B., Zhao, Y., Zhang, C., Abbasi, A.R., Ferrando, S., Dai, R., et al. (2015)Surface architecture of the olfactory epithelium of two Chinese cave loaches (Cypriniformes: Nemacheilidae: Oreonectes).
Waryani. B., Zhao, Y., Zhang, C., Abbasi, A.R., Ferrando, S., Dai, R., et al. (2015)Surface architecture of the olfactory epithelium of two Chinese cave loaches (Cypriniformes: Nemacheilidae: Oreonectes).
Waryani. B., Zhao, Y., Zhang, C., Abbasi, A.R., Ferrando, S., Dai, R., et al. (2015)Surface architecture of the olfactory epithelium of two Chinese cave loaches (Cypriniformes: Nemacheilidae: Oreonectes).
Waryani. B., Zhao, Y., Zhang, C., Abbasi, A.R., Ferrando, S., Dai, R., et al. (2015)Surface architecture of the olfactory epithelium of two Chinese cave loaches (Cypriniformes: Nemacheilidae: Oreonectes).
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Liu, Z., Wen, H., Hailer, F., Dong, F., Yang, Z., Liu, T., Han, L., Shi, F., Hu, Y. and Zhou, J. (2019)Pseudogenization of Mc1r gene associated with transcriptional changes related to melanogenesis explains leucistic phenotypes in Oreonectes cavefish (Cypriniformes, Nemacheilidae)
Liu, Z., Wen, H., Hailer, F., Dong, F., Yang, Z., Liu, T., Han, L., Shi, F., Hu, Y. and Zhou, J. (2019)Pseudogenization of Mc1r gene associated with transcriptional changes related to melanogenesis explains leucistic phenotypes in Oreonectes cavefish (Cypriniformes, Nemacheilidae)
Liu, Z., Wen, H., Hailer, F., Dong, F., Yang, Z., Liu, T., Han, L., Shi, F., Hu, Y. and Zhou, J. (2019)Pseudogenization of Mc1r gene associated with transcriptional changes related to melanogenesis explains leucistic phenotypes in Oreonectes cavefish (Cypriniformes, Nemacheilidae)
Liu, Z., Wen, H., Hailer, F., Dong, F., Yang, Z., Liu, T., Han, L., Shi, F., Hu, Y. and Zhou, J. (2019)Pseudogenization of Mc1r gene associated with transcriptional changes related to melanogenesis explains leucistic phenotypes in Oreonectes cavefish (Cypriniformes, Nemacheilidae)
Huang, J.Q., Yang, J., Wu, Z.Q. and Zhao, Y.H. (2019)Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China
Huang, J.Q., Yang, J., Wu, Z.Q. and Zhao, Y.H. (2019)Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China
Huang, J.Q., Yang, J., Wu, Z.Q. and Zhao, Y.H. (2019)Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China
Huang, J.Q., Yang, J., Wu, Z.Q. and Zhao, Y.H. (2019)Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
Liu, Z., Qian, X., Wang, Z., Wen, H., Han, L. and Zhou, J. (2021)First draft genome of loach (Orenectes shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish
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Zhao, L.-X., Liu, J.-H., Du, L.N. and Luo, F.G. (2021)A new loach species of Troglonectes (Teleostei: Nemacheilidae) from Guangxi, China
Wang, Y.L. (2022)Systematic Taxonomy of the Genus Oreonectes and Troglonectes
Luo, T., Yang, Q., Wu, L., Wang, Y.-L., Zhou, J.-J., Deng, H.Q., Xiao, N. and Zhou, J. (2023)Phylogenetic relationships of Nemacheilidae cavefish (Heminoemacheilus, Oreonectes, Yunnanilus, Paranemachilus, and Troglonectes) revealed by analysis of mitochondrial genome and seven nuclear genes