Chromosome‐level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater

Abstract

Gadiformes includes some of the most important commercial fish (e.g., cod, hake, and haddock) worldwide and accounts for approximately 18% of the world's total marine fish catch (FAO, 2004).Gadiform fish inhabit cold waters in every high-latitude oceans from deep-sea benthic habitats to coastal waters. Only one species in this order, that is, the burbot (Lota lota), is in freshwater habitats (Nelson, 1994). However, to date, the only available high-quality genome sequences of the Gadiformes species are for Atlantic cod (Gadus morhua; Kirubakaran et al., 2020;Tørresen et al., 2017) and haddock (Melanogrammus aeglefinus;Tørresen et al., 2018), and this limitation considerably hinders the taxonomical, evolutionary, and biological studies of the order Gadiformes.The burbot is the only member of the cod family (Gadidae) adapted solely to freshwater (Figure 1; Schaefer et al., 2016). This fish has a wide holarctic distribution, showing the widest longitudinal range among freshwater fish worldwide. The burbot is distributed in nearly all suitable freshwater basins of North America,

Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies

“…The final genome assembly was 583.78 Mb, with a contig N50 of 9.08 Mb, and a scaffold N50 of 21.89 Mb ( Table 1 ). In comparison with a recently released burbot genome assembly by Han et al (2021) , it was suggested that the genome assembled in this study has better quality for higher contig N50 and more accurate chromosome number ( Supplementary Table 4 ). The contig N50 of the genome assembled by Han et al (2021) was 2.01 Mb, and the assembled sequences were anchored to 22 pseudochromosomes, which might be attributed to a low resolution of Hi-C assembly or chromosome loss or fusion caused by local adaptation.…”

“…In comparison with a recently released burbot genome assembly by Han et al (2021) , it was suggested that the genome assembled in this study has better quality for higher contig N50 and more accurate chromosome number ( Supplementary Table 4 ). The contig N50 of the genome assembled by Han et al (2021) was 2.01 Mb, and the assembled sequences were anchored to 22 pseudochromosomes, which might be attributed to a low resolution of Hi-C assembly or chromosome loss or fusion caused by local adaptation. A total length of 537.89 Mb of the genomic sequence was anchored, accounting for 92.1% of the entire assembly ( Supplementary Table 5 ).…”

Large-scale Phylogenomic Analysis Provides New Insights Into the Phylogeny of the Order Gadiformes and Evolution of Freshwater Gadiform Species Burbot (Lota lota)

“…Genomic and transcriptomic data for 40 species representing 8 gadiform families and 2 outgroup species (i.e., Cyttopsis rosea and Zeus faber) from the order Zeiformes were retrieved from the NCBI database (Table 1). A new genome assembly of L. lota from Amur River, China was included in this study [29].…”

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

“… 29–31 Chromosome-level genomes have also been reported in catfishes, such as channel catfish ( Ictalurus punctatus ), 32 yellow catfish ( Pelteobagrus fulvidraco ), 33 giant devil catfish ( Bagarius yarrelli ), 34 Southern catfish ( Silurus meridionalis ), 35 Chinese longsnout catfish ( Leiocassis longirostris ), 36 striped catfish ( Pangasianodon hypophthalmus ), 37 and redtail catfish ( Hemibagrus wyckioides ). 38 These chromosome-level assemblies have been widely used as reliable reference genomes for studies of many fields, including ecological adaptation, 35 , 39 , 40 genome evolution, 41–43 gene evolution, 44 , 45 immunology, 46–48 and identification of target-trait-related genes, 49 , 50 in aquatic animals. Moreover, chromosome-level genomes have also been used for studies on sex determination mechanisms, including identification of sex determination regions and genes, 51–53 sex reversal, 54 , 55 and sex chromosome evolutions.…”