Chromosomal assembly of the Antarctic toothfish (<i>Dissostichus mawsoni</i>) genome using third-generation DNA sequencing and Hi-C technology

Abstract

The Antarctic toothfish, Dissostichus mawsoni , belongs to the Nototheniidae family and is distributed in sub-zero temperatures below S60° latitude in the Southern Ocean. Therefore, it is an attractive model species to study the stenothermal cold-adapted character state. In this study, we successfully generated highly contiguous genome sequences of D. mawsoni , which contained 1 062 scaffolds with a N50 length of 36.98 Mb and longest scaffold length of 46.82 Mb. Repetitive elements accounted for 40.87% of the genome. We also inferred 32 914 protein-coding genes using in silico gene prediction and transcriptome sequencing and detected splicing variants using Isoform-Sequencing (Iso-Seq), which will be invaluable resource for further exploration of the adaptation mechanisms of Antarctic toothfish. This new high-quality reference genome of D. mawsoni provides a fundamental resource for a deeper understanding of cold adaptation and conservation of species.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation

“…A long-read assembly of Chaenocephalus aceratus (blackfin icefish) revealed 11 afgps 15 . The locus is also found to be highly fragmented in a recent chromosome-level genome assembly of D. mawsoni 57 , once more demonstrating the challenge of assembling this region. Our assemblies also include finer mapping of co-localised, and potentially co-evolving, gene families such as the trypsinogen genes, and tracking of the evolution of the chimeric intermediate gene ( afgp/tlp ).…”

“…Using five new long-read assemblies, we achieved the contiguous assembly of both LA and MN haemoglobin gene clusters for most of the species, including their flanking genes 62 , 65 , and compared these with four published assemblies for three notothenioids ( Eleginops maclovinus 32 , D. mawsoni 57 , and C. aceratus 15 ) and one temperate non-notothenioid perciform ( Perca flavescens 66 ) (Fig. 5a , Supplementary Fig.…”

“…To study haemoglobin genes in notothenioid species we focused on the five species ( C. gobio, T. bernacchii, H. antarcticus, G. acuticeps , and P. georgianus ) assembled with PacBio data, along with three previously published assemblies ( D. mawsoni 57 , E. maclovinus 32 , and C. aceratus 15 ) to provide as good a clade coverage as possible. The reference genome assembly of the yellow perch (Perca flavescens ) 66 , a close relative to notothenioids within the order Perciformess 9 , was used as a reference to determine haemoglobin gene exon boundaries.…”

Pathways to polar adaptation in fishes revealed by long‐read sequencing

“…We used this combined Actinopterygii + O. amberensis library to annotate REs in the O. amberensis assembly using repeatmasker version 4.1.0 with the search engine set to “ncbi” and the ‐xsmall option. We repeated the above steps to classify and annotate REs in nine additional fish genome assemblies— Chaenocephalus aceratus (Chaenocephalus aceratus V1.0; Kim et al, 2019), Cottoperca gobio (Cottoperca gobio V1.0; Bista et al, 2020), Danio rerio (Danio rerio V4.0; Howe et al, 2013), Dissostichus mawsoni (Dissostichus mawsoni V1.0; Lee et al, 2021), Gadus morhua (gadMor1, Ensembl release 97; Star et al, 2011), Gasterosteus aculeatus (BROAD S1, Ensembl release 97; Jones et al, 2012), Notothenia coriiceps (Notothenia coriiceps V1.0; Shin et al, 2014), Parachaenicthys charcoti (Parachaenichthys charcoti V1.0, GigaDB data set #100321; Ahn et al, 2017) and Takifugu rubripes (FUGU5, Ensembl release 98; Aparicio et al, 2002)—such that each assembly was annotated using a combined library of Actinopterygii and the custom library from repeatmodeler for each species. We summarized repeat abundance by parsing output from repeatmasker and generating plots in R version 3.5.1 (R Core Team, 2021) using custom scripts.…”

Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia blennieEleginops maclovinus- the closest ancestral proxy of Antarctic cryonotothenioids

“…We used the SYNOLOG software [41,42] to evaluate conserved synteny and determine orthologous chromosomes between E. maclovinus and other notothenioid species. A total of ten notothenioid genomes were used for comparisons against E. maclovinus, which include the basal, non-Antarctic Cottoperca gobio (Bovichtidae) [25], five red-blooded cryonotothenioids across four different families (Trematomus bernacchii (Nototheniidae), Dissostichus mawsoni (Nototheniidae) [43], Gymnodraco acuticeps (Bathydraconidae) [21], Harpagifer antarcticus (Harpagiferidae) [21], and Pogonophryne albipinna (Artedidraconidae) (NCBI GCA_028583405.1), and four white-blooded icefishes (Channichthyidae;…”