Genomics of cold adaptations in the Antarctic notothenioid fish radiation ...

• Main Authors: Bista, Iliana, Wood, Jonathan, Desvignes, Thomas, McCarthy, Shane, Matschiner, Michael, Ning, Zemin, Tracey, Alan, Torrance, James, Sims, Ying, Chow, William, Smith, Michelle, Oliver, Karen, Haggerty, Leanne, Salzburger, Walter, Postlethwait, John H., Howe, Kerstin, Clark, Melody S., Detrich, H. William, Cheng, C.-H. Christina, Miska, Eric, Durbin, Richard
• Format: Dataset
• Language: English
• Published: Dryad 2022
• Subjects: FOS: Biological sciences; notothenioids; Phylogenetics; Comparative genomics; Antarctic; Southern Ocean; The Antarctic; Antarc*
• Online Access: https://dx.doi.org/10.5061/dryad.80gb5mktn; https://datadryad.org/stash/dataset/doi:10.5061/dryad.80gb5mktn

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of ... : Phylogenetic analysis was performed using single copy ortholog genes identified with BUSCO, for the 24 newly sequenced notothenioid genomes and 17 previously published genomes of seven notothenioids and ten further species of percomorph fishes. BUSCO (v2) was run with lineage “actinopterygii_odb9”, and the sequences of single- opy orthologs identified in each assembly and extracted for use in further analysis. We used MAFFT v.7.453 to align 266 selected BUSCO genes that were single copy in our annotated gene sets. The 266 alignments were inspected by eye, and apparently misaligned sequence regions were set to missing data. A total of 1,141,524 amino acids were set to missing out of 6,410,688, including nine alignments that were excluded completely, leaving 257 alignments for further analysis. We then aligned nucleotide sequences of the same BUSCO genes according to the amino-acid alignments, ensuring that regions corresponding to the removed sequences were again set to missing data in the nucleotide sequence ...