title: Presence of two tumor necrosis factor (tnf)-α homologs on different chromosomes of zebrafish (Danio rerio) and medaka (Oryzias latipes).
abstract: Two or more isoforms of several cytokines including tumor necrosis factors (tnfs) have been reported from teleost fish. Although zebrafish (Danio rerio) and medaka (Oryzias latipes) possess two tnf-α genes, their genomic location and existence are yet to be described and confirmed. Therefore, we conducted in silico identification, synteny analysis of tnf-α and tnf-n from both the fish with that of human TNF/lymphotoxin loci and their expression analysis in zebrafish. We identified two homologs of tnf-α (named as tnf-α1 and tnf-α2) and a tnf-n gene from zebrafish and medaka. Genomic location of these genes was found to be as: tnf-α1, and tnf-n and tnf-α2 genes on zebrafish chromosome 19 and 15 and medaka chromosome 11 and 16, respectively. Several features such as existence of TNF family signature, conservation of genes in TNF loci with human chromosome, phylogenetic clustering and amino acid similarity with other teleost TNFs confirmed their identity as tnf-α and tnf-n. There were a constitutive expression of all three genes in different tissues, and an increased expression of tnf-α1 and -α2 and a varied expression of tnf-n ligand in zebrafish head kidney cells induced with 20 μg mL(-1) LPS in vitro. Our results suggest the presence of two tnf-α homologs on different chromosomes of zebrafish and medaka and correlate this incidence arising from the fish whole genome duplication event.
authors.affiliation: Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Kinoshita
authors.affiliation: Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
authors.forename: Gouranga
authors.initials: G
authors.lastname: Biswas
authors.affiliation: Interdisciplinary Research Organization, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
authors.forename: Tomoya
authors.initials: T
authors.lastname: Kono
authors.affiliation: Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Hikima
authors.affiliation: Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan. Electronic address: m.sakai@cc.miyazaki-u.ac.jp.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Sakai
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D008969:Molecular Sequence Data; D009990:Oryzias / Q000235:genetics*; D010802:Phylogeny; D020033:Protein Isoforms / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013045:Species Specificity; D026801:Synteny / Q000235:genetics; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics*
chemical_list: D017931:DNA Primers; D020033:Protein Isoforms; D014409:Tumor Necrosis Factor-alpha
keywords: Chromosome systeny; Genome duplication; Genomic location; Medaka; TNF-α; Zebrafish