Genomic organization of the zebrafish (Danio rerio) T cell receptor alpha/delta locus and analysis of expressed products.
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abstract
In testing the hypothesis that all jawed vertebrate classes employ immunoglobulin heavy chain V (IgHV) gene segments in their T cell receptor (TCR) encoding loci, we found that some basic characterization was required of zebrafish TCR. We began by annotating and characterizing the TCR/ locus of Danio rerio based on the most recent genome assembly, GRCz10. We identified a total of 141 theoretically functional V segments which we grouped into 41 families based upon 70% nucleotide identity. This number represents the second greatest count of apparently functional V genes thus far described in an antigen receptor locus with the exception of cattle TCR/. Cloning, relative quantitative PCR, and deep sequencing results corroborate that zebrafish do express TCR, but these data suggest only at extremely low levels and in limited diversity in the spleens of the adult fish. While we found no evidence for IgH-TCR rearrangements in this fish, by determining the locus organization we were able to suggest how the evolution of the teleost / locus could have lost IgHVs that exist in sharks and frogs. We also found evidence of surprisingly low TCR expression and repertoire diversity in this species.
