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.