Journal Article
The telomere-to-telomere genome assembly of the Triplophysa erythraea (Nemacheilidae hypogean fishes)
Wang, C., Yang, X., Liu, D., Suo, W., Li, H., Pu, J., Liu, X., Ku, Q., Yuan, X., Zhou, Y., Gu, Q. and Ou, D.
Record Number:
7067
Year:
2025
Journal:
Scientific Data
Notes:
© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License
Abstract:
Triplophysa erythraea, a distinctive blind cave fish endemic to Hunan's karst caves, faces significant threats due to its restricted range and fragile habitat. The high-quality genome assembly offers essential data for developing conservation strategies, and could be helpful to reveal adaptive mechanisms along with functional drivers behind T. erythraea's unique morphological traits. In this study, we successfully assembled the telomere-to-telomere (T2T) genome of T. erythraea. The genome size was 757.23 Mb, with a contig N50 size of 27.63 Mb and a scaffold N50 size of 29.01 Mb. The Hi-C assembly placed 97.5% of the sequences onto 25 pseudo-chromosomes. Remarkably, 19 chromosomes were assembled into contiguous, gap-free scaffolds. Furthermore, 378.05 Mb (49.93%) of repetitive sequences and 25,179 protein-coding genes were identified, and 99.09% of the protein-coding genes were annotated. Comparative genomic analysis confirmed the genome's high completeness, continuity, and accuracy. The genomic quality was further substantiated by a QV of 51.03 and a 98.38% of BUSCO completeness rate, assessed against the T. erythraea T2T genome assembly. This study serves as a key genetic resource for Nemacheilidae hypogean fishes and will be highly valuable for delineating adaptive genetic mechanisms of cave-adapted Triplophysa stone loaches
Times Cited:
1
Relevent Species:
Related Records:
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
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
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.
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
He, Y. and He, D.K. (2023)X-ray microtomography study of cranium, pectoral fin and girdle, and Weberian Apparatus development in juvenile Triplophysa stewarti (Nemacheilidae)
Wang, Y.D., Dong, X.Y. and Liu, H.B. (2024)The complete mitochondrial genome of Triplophysa erythraea (Huang et al. 2019)(Cypriniformes, Nemacheilidae)
Song, S., Cao, J., Xiang, H., Liu, Z. and Jiang, W. (2025)Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes:
Nemacheilidae): novel gene tandem duplication and evolutionary implications
Wang, C., Yang, X., Liu, D., Suo, W., Li, H., Pu, J., Liu, X., Ku, Q., Yuan, X., Zhou, Y., Gu, Q. and Ou, D. (2025)The telomere-to-telomere genome assembly of the Triplophysa erythraea (Nemacheilidae hypogean fishes)