School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
Genome Biol. 2023 Jan 23;24(1):13. doi: 10.1186/s13059-022-02838-0.
The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.
Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.
Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
澳大利亚黑天鹅（Cygnus atratus）是一种具有鲜明对比羽毛的标志性物种，与亲缘关系密切的北半球白天鹅不同。黑天鹅相对的地理隔离可能导致其免疫 repertoire 有限，易感染传染病，特别是澳大利亚很少接触的传染病。与绿头鸭和疣鼻天鹅（Cygnus olor）不同，黑天鹅对高致病性禽流感极为敏感。由于缺乏可用的天鹅基因组和转录组信息，对这种敏感性的理解受到了阻碍。
在这里，我们利用为脊椎动物物种生成的基于长读的管道生成了第一个具有转录组数据注释的染色体长度的黑天鹅和疣鼻天鹅基因组。我们利用这些基因组和转录组表明，与其他野生水禽不同，黑天鹅缺乏扩展的免疫基因 repertoire，在内皮细胞中缺乏关键的病毒模式识别受体，并且对高致病性禽流感的炎症反应控制不佳。我们还表明，SLC45A2 基因的遗传差异导致了黑天鹅标志性的羽毛。
总之，这些数据表明，黑天鹅的免疫系统使得，如果任何禽病毒感染在其原生栖息地建立，黑天鹅将处于巨大的危险之中。
