Comprehensive genome‑wide analysis of the chicken heat shock protein family: identification, genomic organization, and expression profiles in indigenous chicken with highly pathogenic avian influenza infection

• Published in: BMC genomics Vol. 24; no. 1; p. 793
• Main Authors: Truong, Anh Duc, Tran, Ha Thi Thanh, Chu, Nhu Thi, Nguyen, Huyen Thi, Phan, Lanh, Phan, Hoai Thi, Vu, Thi Hao, Song, Ki-Duk, Lillehoj, Hyun S, Hong, Yeong Ho, Dang, Hoang Vu
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 20-12-2023; BioMed Central; BMC
• Subjects: Amino acids; Analysis; Animals; Apoptosis; Avian flu; Avian influenza; Chick Embryo; Chicken; Chickens; Chickens - genetics; Chickens - metabolism; Chromosomes; Communicable Diseases; Diseases; E coli; Embryogenesis; Embryonic development; Embryonic growth stage; Environmental stress; Expression profile; Gene expression; Gene mapping; Gene sequencing; Genes; Genetic aspects; Genome-wide analysis; Genomes; Genomics; Growth; Health aspects; Heat shock proteins; Heat stress; Heat tolerance; Heat-Shock Proteins - genetics; Heat-Shock Proteins - metabolism; HSP genes; Immune response; Immune system; Infections; Infectious diseases; Influenza; Influenza in Birds - genetics; Intracellular; Intracellular signalling; Methods; Phylogenetics; Phylogeny; Poultry; Prevention; Proteins; Risk factors; RNA; RNA sequencing; Signal transduction; Structural analysis; Temperature effects; Vietnam; United States; Heat shock proteins; Expression profile; Chicken; HSP genes; Genome-wide analysis
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09908-y

Heat shock proteins (HSPs) function as molecular chaperones with critical roles in chicken embryogenesis, immune response to infectious diseases, and response to various environmental stresses. However, little is known on HSP genes in chicken. In this study, to understand the roles of chicken HSPs, we performed genome-wide identification, expression, and functional analyses of the HSP family genes in chicken.
A total of 76 HSP genes were identified in the chicken genome, which were further classified into eight distinct groups (I-VIII) based on phylogenetic tree analysis. The gene-structure analysis revealed that the members of each clade had the same or similar exon-intron structures. Chromosome mapping suggested that HSP genes were widely dispersed across the chicken genome, except in chromosomes 16, 18, 22, 25, 26, and 28-32, which lacked chicken HSP genes. On the other hand, the interactions among chicken HSPs were limited, indicating that the remaining functions of HSPs could be investigated in chicken. Moreover, KEGG pathway analysis showed that the HSP gene family was involved in the regulation of heat stress, apoptotic, intracellular signaling, and immune response pathways. Finally, RNA sequencing data revealed that, of the 76 chicken HSP genes, 46 were differentially expressed at 21 different growth stages in chicken embryos, and 72 were differentially expressed on post-infection day 3 in two indigenous Ri chicken lines infected with highly pathogenic avian influenza.
This study provides significant insights into the potential functions of HSPs in chicken, including the regulation of apoptosis, heat stress, chaperone activity, intracellular signaling, and immune response to infectious diseases.