tetano
Editor, Senior Moderator
Anim Biosci
. 2022 Nov 14.
doi: 10.5713/ab.22.0277. Online ahead of print.
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
Anh Duc Truong[SUP] 1 [/SUP], Ha Thi Thanh Tran[SUP] 1 [/SUP], Nhu Thi Chu[SUP] 1 [/SUP], Huyen Thi Nguyen[SUP] 1 [/SUP], Hao Thi Vu[SUP] 2 [/SUP], Yeojin Hong[SUP] 2 [/SUP], Ki-Duk Song[SUP] 3 [/SUP], Hoang Vu Dang[SUP] 1 [/SUP], Yeong Ho Hong[SUP] 2 [/SUP]
Affiliations
Abstract
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 MAPK proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. KEGG 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 qRT-PCR 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.
Keywords: Chicken; Expression Profile; Fibroblast Growth Factor; Genome-wide Analysis.
. 2022 Nov 14.
doi: 10.5713/ab.22.0277. Online ahead of print.
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
Anh Duc Truong[SUP] 1 [/SUP], Ha Thi Thanh Tran[SUP] 1 [/SUP], Nhu Thi Chu[SUP] 1 [/SUP], Huyen Thi Nguyen[SUP] 1 [/SUP], Hao Thi Vu[SUP] 2 [/SUP], Yeojin Hong[SUP] 2 [/SUP], Ki-Duk Song[SUP] 3 [/SUP], Hoang Vu Dang[SUP] 1 [/SUP], Yeong Ho Hong[SUP] 2 [/SUP]
Affiliations
- PMID: 36397707
- DOI: 10.5713/ab.22.0277
Abstract
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 MAPK proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. KEGG 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 qRT-PCR 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.
Keywords: Chicken; Expression Profile; Fibroblast Growth Factor; Genome-wide Analysis.