The chromosome-level genome ofTriplophysa dalaica(Cypriniformes: Cobitidae) provides insights into its survival in
extremely alkaline environment
Chuanjiang Zhou* , Bo Hu, Yongtao Tang, Changxing Yang, Wenwen
Ma, Xi Wang, Ruyao Liu, Xuemeng Yan, Jing Dong, Xianfeng Wang, Guoxing
Nie*
College of Fisheries, Engineering Technology Research Center of Henan
Province for Aquatic Animal Cultivation, Henan Normal University,
Xinxiang 453007, Henan, China
* Corresponding authors:
College of Fisheries, Henan Normal University, 46 Jian She Dong Road,
Xinxiang, Henan, China
E-mail: niegx@htu.cn or chuanjiang88@163.com Abstract
Lake Dali Nur, located in Inner Mongolia, North China, is alkaline, withTriplophysa dalaica one of the three fish species that not only
survive, but thrive, in the lake. To investigate the presence of
molecular mutations potentially responsible for this adaptation, the
whole genome sequence of the species endemic to the lake was sequenced.
A total of 126.5 Gb and 106 Gb data, covering nearly 200X of the
estimated genome, were generated using long-read sequencing and Hi-C
technology, respectively. De novo assembly generated a genome totalled
607.91 Mb, with a contig N50 of 9.27 Mb. Nearly all whole genome
sequences were anchored and oriented onto 25 chromosomes, with telomeres
for most chromosomes also being recovered. Repeats comprised
approximately 35.01% of the whole genome. A total of 23,925
protein-coding genes were predicted, within which, 98.62% could be
functionally annotated. Through comparisons of T. dalaica ,T. tibetana , and T. siluroides gene models, a total of 898
genes were identified as likely being subjected to positive selection,
with several of them potentially associated with alkaline adaptation,
such as sodium bicarbonate cotransporter, SLC4A4 . Demographic
analyses suggested that the Dali population might have diverged from
endemic freshwater Hai River populations, approximately 1 million years
ago.
The high-quality T. dalaica genome, sequenced in this study, not
only aids in the analyses of alkaline adaptation, but may also assist in
revealing the mysteries of the highly divergent genusTriplophysa .