title: A genomic analysis of chicken cytokines and chemokines.
abstract: As most mechanisms of adaptive immunity evolved during the divergence of vertebrates, the immune systems of extant vertebrates represent different successful variations on the themes initiated in their earliest common ancestors. The genes involved in elaborating these mechanisms have been subject to exceptional selective pressures in an arms race with highly adaptable pathogens, resulting in highly divergent sequences of orthologous genes and the gain and loss of members of gene families as different species find different solutions to the challenge of infection. Consequently, it has been difficult to transfer to the chicken detailed knowledge of the molecular mechanisms of the mammalian immune system and, thus, to enhance the already significant contribution of chickens toward understanding the evolution of immunity. The availability of the chicken genome sequence provides the opportunity to resolve outstanding questions concerning which molecular components of the immune system are shared between mammals and birds and which represent their unique evolutionary solutions. We have integrated genome data with existing knowledge to make a new comparative census of members of cytokine and chemokine gene families, distinguishing the core set of molecules likely to be common to all higher vertebrates from those particular to these 300 million-year-old lineages. Some differences can be explained by the different architectures of the mammalian and avian immune systems. Chickens lack lymph nodes and also the genes for the lymphotoxins and lymphotoxin receptors. The lack of functional eosinophils correlates with the absence of the eotaxin genes and our previously reported observation that interleukin- 5 (IL-5) is a pseudogene. To summarize, in the chicken genome, we can identify the genes for 23 ILs, 8 type I interferons (IFNs), IFN-gamma, 1 colony-stimulating factor (GM-CSF), 2 of the 3 known transforming growth factors (TGFs), 24 chemokines (1 XCL, 14 CCL, 8 CXCL, and 1 CX3CL), and 10 tumor necrosis factor superfamily (TNFSF) members. Receptor genes present in the genome suggest the likely presence of 2 other ILs, 1 other CSF, and 2 other TNFSF members.
authors.affiliation: Institute for Animal Health, Compton, Berkshire RG20 7NN, U.K. pete.kaiser@bbsrc.ac.uk
authors.forename: Pete
authors.initials: P
authors.lastname: Kaiser
authors.forename: Tuang Yeow
authors.initials: TY
authors.lastname: Poh
authors.forename: Lisa
authors.initials: L
authors.lastname: Rothwell
authors.forename: Stuart
authors.initials: S
authors.lastname: Avery
authors.forename: Sucharitha
authors.initials: S
authors.lastname: Balu
authors.forename: Uday S
authors.initials: US
authors.lastname: Pathania
authors.forename: Simon
authors.initials: S
authors.lastname: Hughes
authors.forename: Marianne
authors.initials: M
authors.lastname: Goodchild
authors.forename: Shaun
authors.initials: S
authors.lastname: Morrell
authors.forename: Michael
authors.initials: M
authors.lastname: Watson
authors.forename: Nat
authors.initials: N
authors.lastname: Bumstead
authors.forename: Jim
authors.initials: J
authors.lastname: Kaufman
authors.forename: John R
authors.initials: JR
authors.lastname: Young
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D018925:Chemokines / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D016207:Cytokines / Q000737:chemistry / Q000235:genetics*; D023281:Genomics; D006801:Humans; D007249:Inflammation / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D019707:Receptors, Chemokine / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D018925:Chemokines; D016207:Cytokines; D019707:Receptors, Chemokine