Journal Article
Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau
Yang, X., Liu, H., Ma, Z., Zou, Y., Zou, M., Mao, Y., Li, X., Wang, H., Chen, T.,Wang, W. and Yang, R.
Record Number:
4458
Year:
2019
Journal:
Molecular Ecology Resources
Pages:
1027-1036
Volume:
19
Abstract:
Abstract
Triplophysa is an endemic fish genus of the Tibetan Plateau in China. Triplophysa tibetana,
which lives at a recorded altitude of ~4,000 m and plays an important role in the
highland aquatic ecosystem, serves as an excellent model for investigating high‐altitude
environmental adaptation. However, evolutionary and conservation studies of
T. tibetana have been limited by scarce genomic resources for the genus Triplophysa.
In the present study, we applied PacBio sequencing and the Hi‐C technique to assemble
the T. tibetana genome. A 652‐Mb genome with 1,325 contigs with an N50 length
of 3.1 Mb was obtained. The 1,137 contigs were further assembled into 25 chromosomes,
representing 98.7% and 80.47% of all contigs at the base and sequence number
level, respectively. Approximately 260 Mb of sequence, accounting for ~39.8%
of the genome, was identified as repetitive elements. DNA transposons (16.3%), long
interspersed nuclear elements (12.4%) and long terminal repeats (11.0%) were the
most repetitive types. In total, 24,372 protein‐coding genes were predicted in the
genome, and ~95% of the genes were functionally annotated via a search in public
databases. Using whole genome sequence information, we found that T. tibetana
diverged from its common ancestor with Danio rerio ~121.4 million years ago. The
high‐quality genome assembled in this work not only provides a valuable genomic
resource for future population and conservation studies of T. tibetana, but it also lays
a solid foundation for further investigation into the mechanisms of environmental
adaptation of endemic fishes in the Tibetan Plateau.
K E Y W O R D S
assembly, genome, Hi‐C, PacBio, Tibetan Plateau, Triplophysa
Times Cited:
26
Relevent Species:
Triplophysa langpingensis Yang in Lan, Gan, Wu and Yang 2013Triplophysa fengshanensis Lan in Lan, Gan, Wu and Yang 2013Troglonectes dongganensis Yang in Lan, Gan, Wu and Yang 2013Triplophysa tianlinensis Li, Li, Lan and Du 2016Triplophysa yunnanensis Yang in Wu 1990Triplophysa gejiuensis (Chu and Chen 1979) Chen, Yang and Xu 1992Triplophysa xiangxiensis (Yang, Yuan and Liao 1986) Chen, Yang and Xu 1992Triplophysa xichouensis Liu, Pan, Yang and Chen 2017Triplophysa shilinensis Chen and Yang 1992Triplophysa tianxingensis Yang, Li and Chen 2016Triplophysa nandanensis Lan, Yang and Chen 1995Triplophysa aluensis Li and Zhu 2000Triplophysa qiubeiensis Li, Yang, Chen, Tao, Qi and Han 2008Triplophysa microphthalma (Liao and Wang in Liao, Wang and Luo 1997) Kottelat 2012Triplophysa tianeensis Chen, Cui and Yang 2004Triplophysa xiangshuingensis Li 2004Troglonectes lihuensis (Wu, Yang and Lan 2012) Li 2018Troglonectes huanjiangensis Yang, Wu and Lan 2011Troglonectes longibarbatus (Chen, Yang, Sket and Aljancic 1998)Triplophysa rosa Chen and Yang 2005Triplophysa macrocephala Yang, Wu and Yang 2012Troglonectes lingyunensis (Liao, Wang and Luo 1997) Kottelat 2012Triplophysa anshuiensis Wu, Wei, Lan and Du 2018Triplophysa baotianensis Li, Li, Liu and Li in Li, Liu, Li and Li 2018Triplophysa erythraea Liu and Huang in Huang, Zhang, Huang, Wu, Gong, Zhang, Peng and Liu 2019Triplophysa luochengensis Li, Lan, Chen and Du 2017