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

Feng Zhu, Zhong-Tao Yin, Qiang-Sen Zhao, Yun-Xiao Sun, Yu-Chen Jie, Jacqueline Smith, Yu-Ze Yang, David W Burt, Maxwell Hincke, Zi-Ding Zhang, Meng-Di Yuan, Jim Kaufman, Cong-Jiao Sun, Jun-Ying Li, Li-Wa Shao, Ning Yang, Zhuo-Cheng Hou

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Article number1233
Pages (from-to)1-15
Number of pages15
JournalCommunications Biology
Volume6
Issue number1
Early online date6 Dec 2023
DOIs
Publication statusPublished - Dec 2023

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