Introduction
The order Gadiformes includes some of the most important commercial fish (e.g., cod, hake, and haddock) in the world and accounts for approximately 18% of the world’s total marine fish catch (FAO, 2004). Gadiform fish inhabit cold waters in every high-latitude ocean from deep-sea benthic habitats to coastal waters. Only two species in this order are known in freshwater habitats (Nelson, 2006). However, to date, only one high-quality genome sequence of the Gadiformes species, i.e., the Atlantic cod (Gadus morhua  ) (Star et al., 2011), is available, and this limitation significantly hinders the taxonomical, evolutionary, and biological studies of the order Gadiformes.
The burbot Lota lota  is the only member of the cod family (Gadidae) that is adapted solely to freshwater (Schaefer et al., 2016). This fish has a wide holarctic distribution, showing the widest longitudinal range of freshwater fish in the world. The burbot is distributed in nearly all suitable freshwater basins of North America, Europe, and north Asia (Lehtonen, 1998). Although this fish thrives in freshwater, L. lota has retained many characteristics of its marine ancestors (Blabolil et al., 2018), such as preference for cold water, spawning at low temperatures, high fecundity, and a pelagic larval stage. This species spawns during winter or early spring, typically when the water is still ice‐covered, and the water temperatures are between 1 °C and 4 °C (Bergersen et al., 1993). Spawning occurs on fine to gravel substrate in shallow bays or groyne fields in water depths of 0.3 m to 3.0 m (Fredrich & Arzbach, 2002; Eick et al., 2013).
The burbot is apparently an excellent “indicator” species. This species is vulnerable to many environmental changes, in particular, warming water temperatures and pollution (Stapanian et al., 2010). The burbot in marginal habitats may serve as an early indicator of the impacts of climate change on cold-water fish species (Stapanian et al., 2010). However, stocks of the burbot have severely declined in number and distribution during the past century. Many populations are threatened, have been extirpated, or are otherwise in need of conservation measures (Maitland & Lyle, 1990). For example, in Finland, burbot populations have declined or have been destroyed completely in 16% of the lakes (Tammi et al., 1999). A series of threats, including pollution, habitat fragmentation, exploitation, and invasive species, have caused the decline or extirpation of many burbot populations (Stapanian et al., 2010). Genomics resources will support the conservation studies of burbot. Given the widest holarctic distribution of this species, the burbot may undergo some degree of local adaptation, which can be resolved with genome-wide high-quality SNPs. However, the available genetic information for this fish remains scarce. At present, only limited genetic studies have been conducted on the microsatellite loci isolation and population structure of the burbot (Houdt et al., 2005; Sanetra, 2005). Thus, sequencing the genome of the burbot is essential. This process may help to reveal insights into the evolutionary history of the burbot and the role of environmental changes in shaping the genome evolution from marine to freshwater.
The burbot,the only freshwater species in the cod family (Gadidae),represents a classical transition from marine to freshwater. Fossil evidence suggests that the Lota genus has already inhabited European rivers in the early Pliocene (Houdt et al., 2005). This phenomenon indicates that the burbot left the ocean and migrated to the freshwater. The transition from an oceanic to a freshwater habitat provides an opportunity for drastic environmental changes in the ecology, morphology, and behavior of fish. This transition should select numerous functional genes. Marine to freshwater transition events rarely occurs (Finnegan, 2017), which is likely due to physiological and ecological barriers associated with changing environmental conditions. These factors include lower salinity, relatively high levels of UV radiation, dramatic fluctuations in freshwater temperature, and competition from primary freshwater fish lineages. Despite these challenges, several freshwater fish from marine-derived lineages have completed this transition from ocean to freshwater and invaded successfully freshwater habitats. Concerted effort, such as the convergence of their morphological and physiological characters, has been reported to freshwater adaptations (Jara, 1988). The genomic changes underlying a convergent evolution may be reproducible to some extent, and convergent phenotypic traits may commonly arise from the same genetic changes. Physiological convergence is strong in freshwater fish of marine-derived lineages and provides a practical way to identify freshwater adaptations.
In this study, a chromosome-level genome assembly of burbot was constructed by combining short reads, PacBio long reads, and Hi-C sequencing data. The assembly was used to identify the genetic signatures of evolution related to freshwater adaptation in burbot and Perciformes by comparative genomics of 13 distantly related species, including three freshwater Percomorpha species. This study will provide a genomic resource to further address the key evolutionary process of freshwater adaptation for marine-originated species.