The chromosome-level genome of Triplophysa dalaica (Cypriniformes:
Cobitidae) provides insights into its survival in extremely alkaline
environment
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 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 genus
Triplophysa.