Karawita, Anjana C.Cheng, YuanyuanChew, Keng YihChallagulla, ArjunKraus, RobertMueller, Ralf C.Tong, Marcus Z. W.Hulme, Katina D.Bielefeldt-Ohmann, HelleSteele, Lauren E.Wu, MelanieSng, JulianNoye, EllesandraBruxner, Timothy J.Au, Gough G.Lowther, SuzanneBlommaert, JulieSuh, AlexanderMcCauley, Alexander J.Kaur, ParwinderDudchenko, OlgaAiden, ErezFedrigo, OlivierFormenti, GiulioMountcastle, JacquelynChow, WilliamMartin, Fergal J.Ogeh, Denye N.Thiaud-Nissen, FrançoiseHowe, KerstinTracey, AlanSmith, JacquelineKuo, Richard I.Renfree, Marilyn B.Kimura, TakashiSakoda, YoshihiroMcDougall, MathewSpencer, Hamish G.Pyne, MichaelTolf, ConnyWaldenström, JonasJarvis, Erich D.Baker, Michelle L.Burt, David W.Short, Kirsty R.2023-02-232023-02-232023Karawita, Anjana C., Cheng, Yuanyuan, Chew, Keng Yih, et al.. "The swan genome and transcriptome, it is not all black and white." <i>Genome Biology,</i> 24, (2023) Springer Nature: https://doi.org/10.1186/s13059-022-02838-0.https://hdl.handle.net/1911/114480Background: 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. Results: 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. Conclusion: 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.engThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.Journal articles13059-022-02838-0https://doi.org/10.1186/s13059-022-02838-0