Revealing the species-specific genotype of the edible bird’s nest-producing swiftlet, Aerodramus fuciphagus and the proteome of edible bird’s nest

[Display omitted] •The current study has sequenced and assembled the first genome of an edible bird’s nest (EBN) producing swiftlet, Aerodramus fuciphagus.•Coiled-coil domain-containing protein 63 (CCDC63) gene was found to be expanded in A. fuciphagus compared to other avian species and there were 3 paralogous CCDC63 genes in A. fuciphagus.•The current study has identified 398 proteins in EBN and a few of them contained Ca2+ binding epidermal growth factor like (EGF-like) domains.•Acidic mammalian chitinase and lysyl oxidase in EBN were found to be active when extracting with distilled water at room temperature, but not hot distilled water or after simulated gastric digestion. Only a few species of swiftlets in the Aerodramus and Collocalia genera can produce edible bird's nests (EBN). These saliva-cemented nests have been consumed as delicacies for centuries in Asia. Many researches have reported the aqueous extract of EBN has epidermal growth factor-like (EGF-like) activity. However, no standalone EGF has been identified in EBN. Moreover, proteome of EBN remained unclear due to lack of genomic data base of an EBN-producing swiftlet to support proteomic analysis of EBN. To address this, the first genome of the EBN-producing swiftlet, Aerodramus fuciphagus, was constructed. Orthology comparison of A. fuciphagus with 10 other avian species were conducted. The results revealed that the number of predicted paralogous coiled-coil domain-containing protein 63 (CCDC63) coding sequences (CDSs) in A. fuciphagus was found to be significantly expanded in comparison to Gallus gallus. There were 3 paralogous CCDC63 genes in the genome of A.fuciphagus. The CDSs predicted from the genome of A. fuciphagus were used to construct a database for proteomic analysis of EBN. In total, 398 proteins have been identified in EBN. The proteome of EBN was significant enriched with extracellular proteins as well as proteins related to extracellular matrix (ECM) organization and immune response. A few proteins with Ca2+-binding EGF-like domains were found in the proteome of EBN, like fibrillin-1, protocadherin fat 4 and coagulation factor X. No standalone EGF protein was identified. This indicated that the proteins with EGF-like domains might be responsible for the EGF-like activity of EBN. In addition, acidic mammalian chitinase and lysyl oxidase in EBN were found to be active when extracting with distilled water at room temperature. The current study has not just revealed the speci