{
  "abstract": "Background\n\nNotothenioids are a well characterised species flock endemic to the Antarctic and an important model group for studying genome adaptation to extreme cold. A new reference assembly and clade-wide comparative genomic analysis allow for investigation of cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation.Results\n\nA new phased assembly of a model notothenioid, Harpagifer antarcticus, demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the afgp locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the afgp locus expansion in H. antarcticus through segmental tandem duplications involving two pairs of afgp genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation.Conclusions\n\nDiversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.",
  "abstract_shown": true,
  "affiliations": [
    "Senckenberg Research Institute and Natural History Museum, Frankfurt Am Main, Germany.",
    "Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, UK.",
    "Department of Genetics, University of Cambridge, Cambridge, UK.",
    "Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA.",
    "British Antarctic Survey, High Cross, Madingley Road, Cambridge, UK.",
    "Senckenberg Research Institute and Natural History Museum, Frankfurt Am Main, Germany. ilianabista@gmail.com.",
    "Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, UK. ilianabista@gmail.com."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jacopo Martelossi"
    },
    {
      "affs": [
        1
      ],
      "name": "Ksenia Krasheninnikova"
    },
    {
      "affs": [
        1
      ],
      "name": "Amy Denton"
    },
    {
      "affs": [
        1
      ],
      "name": "Jonathan M D Wood"
    },
    {
      "affs": [
        1
      ],
      "name": "Thomas C Mathers"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Richard Durbin"
    },
    {
      "affs": [
        3
      ],
      "name": "Nova Fong"
    },
    {
      "affs": [
        3
      ],
      "name": "David L Bentley"
    },
    {
      "affs": [
        4
      ],
      "name": "Melody S Clark"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Iliana Bista"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/48dx9g623v5c0.bib",
  "cited_by": 0,
  "doi": "10.1186/s13059-026-04293-7",
  "fulltext_url": "https://europepmc.org/articles/PMC13670615",
  "id": "48dx9g623v5c0",
  "issns": [
    "1474-7596",
    "1474-760X"
  ],
  "landing_url": "https://europepmc.org/article/MED/42881419",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1110|Chromosomal and Genetic Variations"
    ]
  ],
  "openalex": "W7222242027",
  "pdf_url": "https://europepmc.org/articles/PMC13670615?pdf=render",
  "pmcid": "PMC13670615",
  "pmid": "42881419",
  "published": "2026-10-15",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/48dx9g623v5c0.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42881419",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42881419"
    },
    {
      "first_seen": "2026-10-30T12:19:06Z",
      "native_id": "10.1186/s13059-026-04293-7",
      "source": "crossref",
      "url": "https://link.springer.com/article/10.1186/s13059-026-04293-7"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1110|Chromosomal and Genetic Variations",
      "subfield": "plant-biology"
    }
  ],
  "title": "A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.",
  "title_text": "A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:06Z",
  "url": "https://research.draconitic.com/paper/48dx9g623v5c0",
  "venue": "Genome biology",
  "versions": []
}