Introduction
Triplophysa dalaica is a member of the family Cobitidae: Cypriniformes. It is widely distributed in northern China, predominately in the trunk and tributaries of the Yellow River, and Inner Mongolia, in artesian waters, such as Lake Dali Nur. This lake is located in an endorheic basin on the eastern Inner Mongolian Plateau, North China, where its alkalinity can rise to 53.57 mmol/L (pH 9.6). It is believed to have expanded to 1,600 km2 during the early Holocene (11,500–7,600 calibrated years BP), due to a mass influx of glacial meltwater from the Greater Khingan Range. Its water level fluctuated dramatically during the middle Holocene and constantly shrank during the late Holocene (3,450 calibrated years BP to present) (Xiao, Si, Zhai, Itoh, & Lomtatidze, 2008). Due to both the perennial sandstorms and dry weather of Inner Mongolia, water of the Dali Lake has been gradually concentrated and salinized. This has resulted in the long-term directional selection of fish in this habitat, with only a small number of special species, such as Carassius auratus Linnaeus,Leuciscus waleckii , and T. dalaica , able to adapt to the highly salinized environment (J. Xu et al., 2013). As T. dalaicacan thrive in the highly alkaline Lake Dali Nur, thus demonstrating their ability to adapt to high basicity tolerance and stress resistance, they are optimal candidates for investigating alkaline resistance mechanisms in fish.
In recent years, salt-alkali water development has intensified significantly in China. Due to their economic value, C. auratusand L. waleckii have always attracted greater attention thanT. dalaica . In L. waleckii , a set of genomic regions, under selective sweeps harboring genes involved in ion homoeostasis, acid-base regulation, unfolded protein response, reactive oxygen species elimination, and urea excretion were detected (J. Xu et al., 2017).
Compared with other saline-tolerant or high-altitude acclimatized fish,T. dalaica reach sexual maturity at an early age, generally at two years of age. Therefore, for alkali-resistant gene inheritance and screening, the research cycle can be significantly shortened. Thirteen candidate genes, including hif-1αB and hif-2αA, have been reported as likely involved in the hypoxia response of T. dalaica , suggesting that genetic mechanisms of adaptation to high-altitude hypoxia could be resolved using RNA sequencing technology (Wang, Yang, Wu, Song, & He, 2015). Triplophysa fish are a strongly diverged group of fish encompassing 137 valid species, as recorded in FishBase (Froese & Pauly, 2014). These fish not only inhabit freshwater environments, but can also survive in saline and alkaline lakes, or at high altitudes, which is ideal for investigating local adaptation and ecological speciation. In recent years, the evolution of high-throughput sequencing techniques has provided new opportunities for elucidating the genetic basis of adaptation and speciation in Triplophysa fish. For example, the whole genome sequence of T. tibetana laid a solid foundation for further investigation into the environmental adaptation mechanisms of endemic fishes in the Tibetan Plateau (X. Yang et al., 2019). The genome assembly of T. siluroides provided genomic resources to better understand Tibetan loach biology, and set a stage for comparative analysis of classification, diversification, and adaptation of fishes in Cobitoidea (L. Yang et al., 2019). However, the molecular mechanisms underlying adaptation to high salt environments in populations ofT. dalaica remain relatively poorly understood.
In this study, we present the chromosome-level genome of T. dalaica, which inhabits the extremely alkaline waters of Lake Dali Nur, using both PacBio long-read sequencing and Hi-C technology. The size of the resultant genome was approximately 607.91 Mb, with a contig N50 size of 9.27 Mb, and a final gene set consisting of 23,925 genes. To detect possible genes related to alkaline adaptation, the final gene set was compared with publicly available gene sets of T. siluroides andT. tibetana . Effective population size dynamics between the alkaline Lake Dali Nur and the freshwater region were also discussed.