A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution

Paris, J. R.; Fernandes, F. A. N.; Santos, C. A.; Pointon, D.-L. B.; Wood, J. M. D.; Obiol, J. F.; Salces-Oritz, J.; Fernandez, R.; Cristofari, R.; Le Bohec, C.; Trucchi, E.

doi:10.1101/2025.03.13.642884

bioRxiv · 10.1101/2025.03.13.642884

A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution

Paris, J. R.·Fernandes, F. A. N.·Santos, C. A.·Pointon, D.-L. B.·Wood, J. M. D.·Obiol, J. F.·Salces-Oritz, J.·Fernandez, R.·Cristofari, R.·Le Bohec, C.·Trucchi, E.

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Abstract

The King penguin (Aptenodytes patagonicus) is an iconic species of the Southern Ocean and is currently being developed as a model-in-the-wild for understanding evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female King penguin - Pen/Se-guin - from the Crozet Archipelago, assembled using PacBio HiFi long-read sequencing and Hi-C proximity data. 94.93% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes), with a BUSCO completeness of 97.2%, a k-mer completeness of 99.7%, and a quality value (QV) of 63.8. We also assembled a circularised mitogenome (20,520 bp), which includes the avian tandem duplication (TD). Annotation of repetitive sequences revealed that 16.3% of the genome comprises repetitive elements, with LINEs being the most abundant transposable element class (5.6%). Gene prediction using an extensive multi-tissue RNA-seq dataset resulted in 18,081 predicted protein-coding genes, of which 17,081 were functionally annotated, with a BUSCO completeness of 98.4% and an OMArk completeness of 97.3%. The presented assembly substantially improves the quality of a previous draft genome, showing a 28-fold increase in assembly contiguity and a significantly improved genome annotation, exceeding the standards of the Earth BioGenome Project (EBP) and Vertebrate Genomes Project (VGP). This high-quality genome will enable ongoing and future studies harnessing the King penguin as a model-in-the-wild to test hypotheses on the genotype-to-fitness link, ageing, life-history trait evolution, and adaptation.

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Paris, J. R., Fernandes, F. A. N., Santos, C. A., Pointon, D.-L. B., Wood, J. M. D., Obiol, J. F., Salces-Oritz, J., Fernandez, R., Cristofari, R., Le Bohec, C., Trucchi, E.. 2025-03-15. A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution. https://doi.org/10.1101/2025.03.13.642884

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