The Chromosome-Level Genome of Triplophysa dalaica (Cypriniformes: Cobitidae) Provides Insights into Its Survival in Extremely Alkaline Environment

Author:

Zhou Chuanjiang1ORCID,Hu Bo1,Tang Yongtao1ORCID,Yang Changxing1,Ma Wenwen1,Wang Xi1,Liu Ruyao1,Yan Xuemeng1,Dong Jing1,Wang Xianfeng1,Nie Guoxing1

Affiliation:

1. College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan, China

Abstract

Abstract Lake Dali Nur, located in Inner Mongolia, North China, is alkaline, with Triplophysa 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 was sequenced. A total of 126.5 and 106 Gb data, covering nearly 200× 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 Ma. The high-quality T. dalaica genome, created in this study, not only aids in the analyses of alkaline adaptation, but may also assist in revealing the mysteries of the highly divergent genus Triplophysa in the future.

Publisher

Oxford University Press (OUP)

Subject

Genetics,Ecology, Evolution, Behavior and Systematics

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