A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes.

Acknowledgements: We thank members of the Poultry Breeding Group of the College of Animal Science and Technology for assisting in the collection of blood samples and rearing of birds. This work was supported by the National Key R&D Program of China (2022YFF1000100), National Natural Science Foundation of China (31572388, 31972525) and China Agriculture Research System of MOF and MARA(CARS-41) to Z.C.H., National Natural Science Foundation of China (No.31930105), National Key Research and Development Program of China(2022YFF1000204) and China Agriculture Research System of MOF and MARA(CARS-40) to N.Y., National Key Research and Development Program of China (2021YFD1300600) to C.J.S. Hincke’s participation was additionally supported by the Canadian Natural Sciences and Engineering Research Council (NSERC, Discovery program RGPIN-2022-04803).Funder: National Key R&D Program of China (2022YFF1000100)A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes