Chromosome-level genome assembly of the King penguin (Aptenodytes patagonicus)

The King penguin (Aptenodytes patagonicus) is the second largest species of penguin and is an iconic species of the Antarctic Circumpolar Region. We present a chromosome-level genome of the King penguin derived from an adult female sampled from Possession Island in the Crozet Archipelago. Using HiFi long-read sequencing and Hi-C proximity data, we assembled a 1.35 Gb genome for the King penguin, comprising 34 chromosomes (32 autosomes, plus the Z and W chromosomes). The assembly is high-quality with a scaffold N50 of 87 Mb, a BUSCO completeness of 97.2% (95.7% as single-copy), a k-mer completeness of 99.7%, and a quality value (QV) of 63.8. Annotation of repetitive sequences revealed that 14.8% of the genome comprises repetitive elements, with LINEs being the most abundant transposable element class (4.2%). Gene prediction using an extensive multi-tissue RNA-seq dataset provided 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. This high-quality, chromosome-level assembly will enable ongoing and future studies investigating the evolution and ecology of the King penguin, including quantifying fitness, ageing, life-history trait evolution and adaptation to climate change.