A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.
7 affiliations
- 1Senckenberg Research Institute and Natural History Museum, Frankfurt Am Main, Germany.
- 2Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, UK.
- 3Department of Genetics, University of Cambridge, Cambridge, UK.
- 4Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA.
- 5British Antarctic Survey, High Cross, Madingley Road, Cambridge, UK.
- 6Senckenberg Research Institute and Natural History Museum, Frankfurt Am Main, Germany. [email protected].
- 7Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, UK. [email protected].
Abstract
Background
Notothenioids 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
A 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
Diversifying 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.
Related
- The haplotype-resolved T2T genome assembly reveals the evolution and adaptation mechanisms of cold resistance in Rosa beggeriana.
- Mapping Evolution of Molecules across Biochemistry with Assembly Theory
- A chromosome-level genome assembly of the classical model nematode Panagrellus redivivus for comparative studies of parasitism evolution
- Evolution of frugivory across a large radiation of non-seed-dispersing animals
- Chromosome-level genome assembly of Falcataria falcata provides insights into ancient polyploidy and duplicate gene evolution in Fabaceae
BibTeX
@article{martelossi2026phased,
title = {{A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.}},
author = {Jacopo Martelossi and Ksenia Krasheninnikova and Amy Denton and Jonathan M D Wood and Thomas C Mathers and Richard Durbin and Nova Fong and David L Bentley and Melody S Clark and Iliana Bista},
journal = {Genome biology},
year = {2026},
month = oct,
doi = {10.1186/s13059-026-04293-7},
url = {https://europepmc.org/article/MED/42881419},
note = {CC BY},
}
RIS
TY - JOUR
TI - A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.
AU - Jacopo Martelossi
AU - Ksenia Krasheninnikova
AU - Amy Denton
AU - Jonathan M D Wood
AU - Thomas C Mathers
AU - Richard Durbin
AU - Nova Fong
AU - David L Bentley
AU - Melody S Clark
AU - Iliana Bista
PY - 2026
DA - 2026/10/15
JO - Genome biology
DO - 10.1186/s13059-026-04293-7
UR - https://europepmc.org/article/MED/42881419
AB - Background Notothenioids 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 A 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 Diversifying 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.
SN - 1474-7596
SN - 1474-760X
ER -