The Australian black swan genome and transcriptome provide insight into the pathogenesis of highly pathogenic avian influenza virus (HPAI).

The plumage of the Australian black swan (Cygnus atratus) is in stark contrast to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may result in a limited immune repertoire and increased susceptibility to infectious disease, including infectious diseases that are common in other parts of the world. Indeed, unlike the ducks and the mute swan, the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome. Here, we generate the first annotated black and mute swan genomes. We use these, combined with the black and mute swan transcriptome, to demonstrate that compared to other wild waterfowl, black swans have not expanded their immune gene repertoire, lack a key viral pattern-recognition receptor and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan.