The chemokinome superfamily: II. The 64 CC chemokines in channel catfish and their involvement in disease and hypoxia responses.
Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. Based on the arrangement of the first four cysteine residues, they are classified into CC, CXC, C and CX3C subfamilies. In this study, a complete set of 64 CC chemokine ligand (CCL) genes was systematically identified, annotated, and characterized from the channel catfish genome. Extensive phylogenetic and comparative genomic analyses supported their annotations, allowing establishment of their orthologies, revealing fish-specific CC chemokines and the expansion of CC chemokines in the teleost genomes through lineage-specific tandem duplications. With 64 genes, the channel catfish genome harbors the largest numbers of CC chemokines among all the genomes characterized to date, however, they fall into 11 distinct CC chemokine groups. Analysis of gene expression after bacterial infections indicated that the CC chemokines were regulated in a gene-specific and time-dependent manner. While only one member of CCL19 (CCL19a.1) was significantly up-regulated after Edwardsiella ictaluri infection, all CCL19 members (CCL19a.1, CCL19a.2 and CCL19b) were significantly induced after Flavobacterium columnare infection. In addition, CCL19a.1, CCL19a.2 and CCL19b were also drastically up-regulated in ESC-susceptible fish, but not in resistant fish, suggesting potential significant roles of CCL19 in catfish immune responses. High expression levels of certain CC appeared to be correlated with susceptibility to diseases and intolerance to hypoxia.
State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China; The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Qiang
Q
Fu
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Yujia
Y
Yang
Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China.
Chao
C
Li
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Qifan
Q
Zeng
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Tao
T
Zhou
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Ning
N
Li
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Yang
Y
Liu
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Yun
Y
Li
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Xiaozhu
X
Wang
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
Shikai
S
Liu
State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.
Daoji
D
Li
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA. Electronic address: liuzhan@auburn.edu.
Zhanjiang
Z
Liu
D000818:Animals; D019742:Chemokines, CC / Q000276:immunology*; D005393:Fish Diseases / Q000235:genetics / Q000276:immunology*; D029941:Fish Proteins / Q000235:genetics / Q000276:immunology; D020869:Gene Expression Profiling; D000860:Hypoxia / Q000235:genetics / Q000276:immunology*; D007059:Ictaluridae / Q000235:genetics / Q000276:immunology*; D007113:Immunity, Innate / Q000235:genetics / Q000276:immunology*; D059467:Transcriptome
D019742:Chemokines, CC; D029941:Fish Proteins
Chemokine; Disease resistance; Fish; Genome; Hypoxia; Innate immunity