Conclusion
Through application of both long-read sequencing and Hi-C technology, we obtained a whole genome sequence assembly of an individual T. dalaica endemic to the alkaline Lake Dali Nur, located in Inner Mongolia, northeast China. The contig N50 length of the assembly exceeded 9 Mb, with nearly all contigs anchored to chromosomes; thus, the assembly was at the chromosome level. Importantly, telomeres were obtained for majority of the chromosomes. A number of assessments, including mapping of the RNA-Seq short reads, BUSCO appraisal, and collinearity with D. rerio and T. tibetana, all suggest high assembly accuracy. Through gene model comparisons of T. dalaica with other fish belonging to Cypriniformes, we found thatT. dalaica was closer to T. tibetana than T. siluroides , with divergence between T. dalaica and T. tibetana occurring more than 8 Mya. Positive selection analyses identified a number of pivotal genes likely related to alkaline adaptation of the species. Demographic analyses suggested that the population of T. dalaica , endemic to Lake Dali Nur, might have diverged approximately 1 Mya from the Hai River population, with different EPS fluctuations likely resulting from different environmental factors.