Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection
Objective Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Asian-Australasian Association of Animal Production Societies
2023-04-01
|
| Series: | Animal Bioscience |
| Subjects: | |
| Online Access: | http://www.animbiosci.org/upload/pdf/ab-22-0277.pdf |
| _version_ | 1811157838122188800 |
|---|---|
| author | Anh Duc Truong Ha Thi Thanh Tran Nhu Thi Chu Huyen Thi Nguyen Thi Hao Vu Yeojin Hong Ki-Duk Song Hoang Vu Dang Yeong Ho Hong |
| author_facet | Anh Duc Truong Ha Thi Thanh Tran Nhu Thi Chu Huyen Thi Nguyen Thi Hao Vu Yeojin Hong Ki-Duk Song Hoang Vu Dang Yeong Ho Hong |
| author_sort | Anh Duc Truong |
| collection | DOAJ |
| description | Objective Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A–F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4–6, 9–10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R2 = 0.92–0.95, p<0.01). Conclusion This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections. |
| first_indexed | 2024-04-10T05:13:04Z |
| format | Article |
| id | doaj.art-ccef0ec3c26742fc9e6e95b6f10ed5d6 |
| institution | Directory Open Access Journal |
| issn | 2765-0189 2765-0235 |
| language | English |
| last_indexed | 2024-04-10T05:13:04Z |
| publishDate | 2023-04-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Animal Bioscience |
| spelling | doaj.art-ccef0ec3c26742fc9e6e95b6f10ed5d62023-03-09T05:50:34ZengAsian-Australasian Association of Animal Production SocietiesAnimal Bioscience2765-01892765-02352023-04-0136457058310.5713/ab.22.027724964Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infectionAnh Duc Truong0Ha Thi Thanh Tran1Nhu Thi Chu2Huyen Thi Nguyen3Thi Hao Vu4Yeojin Hong5Ki-Duk Song6Hoang Vu Dang7Yeong Ho Hong8 Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea The Animal Molecular Genetics and Breeding Center and Department of Animal Biotechnology, JeonBuk National University, Jeonju 54896, Korea Department of Biochemistry and Immunology, National Institute of Veterinary Research, 86 Truong Chinh, Dong Da, Ha Noi 100000, Vietnam Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, KoreaObjective Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A–F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4–6, 9–10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R2 = 0.92–0.95, p<0.01). Conclusion This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.http://www.animbiosci.org/upload/pdf/ab-22-0277.pdfchickenexpression profilefibroblast growth factorgenome-wide analysis |
| spellingShingle | Anh Duc Truong Ha Thi Thanh Tran Nhu Thi Chu Huyen Thi Nguyen Thi Hao Vu Yeojin Hong Ki-Duk Song Hoang Vu Dang Yeong Ho Hong Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection Animal Bioscience chicken expression profile fibroblast growth factor genome-wide analysis |
| title | Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection |
| title_full | Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection |
| title_fullStr | Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection |
| title_full_unstemmed | Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection |
| title_short | Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection |
| title_sort | genome wide identification organization and expression profiles of the chicken fibroblast growth factor genes in public databases and vietnamese indigenous ri chickens against highly pathogenic avian influenza h5n1 virus infection |
| topic | chicken expression profile fibroblast growth factor genome-wide analysis |
| url | http://www.animbiosci.org/upload/pdf/ab-22-0277.pdf |
| work_keys_str_mv | AT anhductruong genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT hathithanhtran genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT nhuthichu genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT huyenthinguyen genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT thihaovu genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT yeojinhong genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT kiduksong genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT hoangvudang genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection AT yeonghohong genomewideidentificationorganizationandexpressionprofilesofthechickenfibroblastgrowthfactorgenesinpublicdatabasesandvietnameseindigenousrichickensagainsthighlypathogenicavianinfluenzah5n1virusinfection |