Introduction
Qinghai-Tibet Plateau (QTP), formed by the collision of the Indian Plate with the Eurasian Plate beginning in Eocene ~50 million years ago (Mya), is often deemed as the Roof of the world or the Third Pole due to its average altitude of over 4, 000 meters and massive glaciers (Harrison, et al. 1992; Molnar, et al. 1993; Yin and Harrison 2000; Tapponnier, et al. 2001; Molnar, et al. 2010). High absolute elevation, high radiation, severe cold, and hypoxia are the main characteristics of extreme environmental conditions on QTP, which greatly threaten the survival of the local creatures, especially the wild plateau fish (Li 1991). Originated from a common ancestor Barbinae, Schizothoracine fishes (Teleostei: Cyprinidae), which distributed extensively in the high-altitude streams, rivers and lakes scattered throughout QTP (Zan, et al. 1985; Yue 2000; Li, et al. 2013), evolve gradually and become highly adapted to life in high-altitude environmental stress, are spectacularly diverse in ploidy, physiological plasticity, and morphological innovations, such as numbers of scales, pharyngeal teeth and barbels (Zhou, et al. 2020). Polyploidy can also be commonly observed in Schizothoracine fishes and is regarded as a successful evolutionary transition of organisms to these extreme environments (Zan, et al. 1985; Leggatt and Iwama 2003; Wang, et al. 2016).
Gymnocypris przewalskii (Kessler 1876, NCBI: txid 369649, Fishbase ID: 55381, Figure 1), otherwise known as the Przewalski’s naked carp or scale-less carp is an endemic tetraploid Schizothoracine fish to Qinghai Lake (3196 m above sea level, a.s.l.) in the northeast margin of QTP (Wood, et al. 2007; Xiong, et al. 2010; Tian, et al. 2019). Relative to organisms at higher altitudes, G. przewalskii is an important link in the evolution of biological plateau adaptation. Qinghai Lake is the largest closed-basin lake in China with no surface water outflows, owning to blocking the channel from Qinghai Lake to Yellow River around the end of the Middle Pleistocene (An, et al. 2006). The lake not only has high-altitude environmental characteristics, such as a low concentration of dissolved oxygen (4.16-6.08 mg/L) and unyielding cold (average annual air temperature ~ -0.1℃), but also has its own unique characteristics of strong alkalinity (carbonate alkalinity approximately 29 mM, pH 9.1-9.5) and a high salinity level (approximately 13 ppt) (Wang, et al. 2003; Xu, et al. 2010; Zhang, et al. 2010; Fu, et al. 2013; Cui, et al. 2016). Due to high evaporative water loss, decreasing water supplies, and extensive water diversion for agricultural use, the salinity and the alkalinity levels are increasing by 7% and 0.5% per year, respectively (Yao, et al. 2016) . Unlike most stenohaline cyprinids, G. przewalskii undergoes an annual spawning migration between the saline-alkaline Qinghai Lake and the freshwater tributary rivers. From March to July, fish migrate to freshwater rivers to spawn and, upon completion of reproduction, return to the lake for the rest of the year (Walker, et al. 1995). This transition from river water to lake water causes profound changes for G. przewalskii , which include an acid-base disturbance, a rapid rise in osmolality, and a rise in the concentrations of all measured plasma ions (Wood, et al. 2007; Yao, et al. 2016). Although historically abundant, the naked carp is facing collapse due to overfishing and destruction of spawning habitat through dam building for irrigation, and has been listed as a national class II endangered species and assessed as being vulnerable (VU) in the new Red List of China’s Vertebrates (Wang and Xie 2009; Jiang, et al. 2016).
G. przewalskii is an important and unique animal model for studying aquatic biological development, genetics, evolution and physiology in highland aquatic areas. This unique environmental adaptability is very important for the study of low-oxygen, high saline-alkaline and low-temperature tolerance of high-altitude fish and the long-term evolution mechanism of aquatic organism with tetraploid genome structure in this extreme environment. We therefore chose to sequence, assemble and annotate the genome and transcriptome of G. przewalskii as an example to reveal geographic isolation of Schizothoracine fishes in Qinghai-tibet plateau lift and understand evolutionary adaptation of G. przewalskii to high altitudes, stressful saline-alkaline water environment.