A chromosome-level genome of the king penguin (Aptenodytes patagonicus): a resource for linking genotype to fitness in a long-lived vertebrate

The king penguin (Aptenodytes patagonicus) is a long-lived seabird of the Southern Ocean that is emerging as a promising model in the wild for studying evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female king penguin (Pen/Se-guin) assembled using PacBio HiFi long-reads and Hi-C proximity data. A total of 95% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes). The primary haplotype has a BUSCO completeness of 97.2%, and across both haplotypes the assembly has a k-mer completeness of 99.7% and a quality value of 63.8. We also assembled a circularised mitogenome (20,520 bp) containing the avian tandem duplication. Repetitive sequence annotation showed that 16.3% of the genome comprises repetitive elements, with LINEs representing 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%. Compared with the previous draft genome, the presented genome shows a 30-fold increase in assembly contiguity and a substantially improved genome annotation, exceeding the standards of the Earth BioGenome Project and Vertebrate Genomes Project. This genome provides a foundation for ongoing and future studies using the king penguin to investigate genotype-fitness relationships, ageing, life-history evolution, and adaptation.