Skip to main content

Advertisement

Springer Nature Link
Log in

Comparative analysis of the chicken TCRα/δ locus

  • Brief Communication
  • Published:
Immunogenetics Aims and scope Submit manuscript

Abstract

The access to whole genome sequences has provided the opportunity to study the evolution and organization of immunologically related genes on a large scale. The genes encoding the T cell receptor (TCR) α and δ chains are part of a complex locus that has shown remarkable conserved organization across different amniote lineages. In this study we have examined and annotated the TCRα/δ locus in chicken (Gallus gallus) and compared it to that of zebra finch (Taeniopygia guttata) and other avian species using the current available genome data. We also analyzed the expressed chicken TCRα/δ transcript repertoire and compared it with that previously described for zebra finch. The analyses conducted in this study show that the TCRα/δ locus in birds has undergone major rearrangements and expansion of the germ line repertoire in chicken, compared to zebra finch. A major expansion of the chicken variable gene repertoire appears to be driven by selection for genes from a limited number of subgroups.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

References

  • Chen CH, Six A, Kubota T, Tsuji S, Kong FK, Göbel TW, Cooper MD (1996) T cell receptors and T cell development. Curr Top Microbiol Immunol 212:37–53

    Article  PubMed  CAS  Google Scholar 

  • Dalloul RA et al (2010) Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8:e1000475

    Article  PubMed  Google Scholar 

  • Davis MM, Chein YH (2008) T cell antigen receptors. In: Paul WE (ed) Fundamental immunology, 6th edn. Lippincott, Philadelphia, pp 313–345

    Google Scholar 

  • Giudicelli V, Chaume D, Lefranc M-P (2005) IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res 33:D256–D261

    Google Scholar 

  • Greenwold MJ, Sawyer RH (2010) Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution. BMC Evol Biol 10:148

    Article  PubMed  Google Scholar 

  • Göbel TW, Chen CL, Lahti J, Kubota T, Kuo CL, Aebersold R, Hood L, Cooper MD (1994) Identification of T-cell receptor alpha-chain genes in the chicken. Proc Natl Acad Sci U S A 91:1094–1098

    Article  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716

    Article  Google Scholar 

  • Koop BF, Wilson RK, Wang K, Vernooij B, Zallwer D, Kuo CL, Seto D, Toda M, Hood L (1992) Organization, structure, and function of 95 kb of DNA spanning the murine T-cell receptor C alpha/C delta region. Genomics 13:1209–1230

    Article  PubMed  CAS  Google Scholar 

  • Kubota T, Wang J, Göbel TW, Hockett RD, Cooper MD, Chen CH (1999) Characterization of an avian (Gallus gallus domesticus) TCR αδ gene locus. J Immunol 163:3858–3866

    PubMed  CAS  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  PubMed  CAS  Google Scholar 

  • Loh EY, Cwirla S, Serafini ET, Phillips JH, Lanier LL (1988) Human T-cell-receptor d chain: genomic organization, diversity, and expression in populations of cells. Proc Natl Acad Sci U S A 85:9714–9718

    Article  PubMed  CAS  Google Scholar 

  • Parra ZE, Baker ML, Hathaway J, Lopez AM, Trujillo J, Sharp A, Miller RD (2008) Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 9:111

    Article  PubMed  Google Scholar 

  • Parra ZE, Ohta Y, Criscitiello MF, Flajnik MF, Miller RD (2010) The dynamic TCRδ: TCRδ chains in the amphibian Xenopus tropicalis utilize antibody-like V genes. Eur J Immunol 40:2319–2329

    Article  PubMed  CAS  Google Scholar 

  • Parra ZE, Mitchell K, Dalloul RA, Miller RD (2012) A second TCRδ locus in Galliformes uses antibody-like V domains: insight into the evolution of TCRδ and TCRμ genes in tetrapods. J Immunol 188:3912–3919

    Article  PubMed  CAS  Google Scholar 

  • Rast JP, Anderson MK, Strong SJ, Luer C, Litman RT, Litman GW (1997) Alpha, beta, gamma, and delta T cell antigen receptor genes arose early in vertebrate phylogeny. Immunity 6:1–11

    Article  PubMed  CAS  Google Scholar 

  • Reinink P, Rhijn IV (2009) The bovine T cell receptor alpha/delta locus contains over 400 V genes and encodes V genes without CDR2. Immunogenetics 61:541–549

    Article  PubMed  CAS  Google Scholar 

  • Satyanarayana K, Hata S, Devlin P, Roncarolo MG, De Vries JE, Spits H, Strominger JL, Krangel MS (1988) Genomic organization of the human T-cell antigen-receptor α/δ locus. Proc Natl Acad Sci U S A 85:8166–8170

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  • Triebel F, Faure F, Mami-Chouaib F, Jitsukawa S, Griscelli A, Genevée C, Roman-Roman S, Hercend T (1988) A novel human Vδ gene expressed predominantly in the TiγA fraction of γ/δ+ peripheral lymphocytes. Eur J Immunol 18:2021–2027

    Article  PubMed  CAS  Google Scholar 

  • Uenishi H, Hiraiwa H, Yamamoto R, Yasue H, Takagaki Y, Shiina T, Kikkawa E, Inoko H, Awata T (2003) Genomic structure around joining segments and constant regions of swine T-cell receptor α/δ (TRA/TRD) locus. Immunology 109:515–526

    Article  PubMed  CAS  Google Scholar 

  • Van Tuinen M, Hedges SB (2001) Calibration of avian molecular clocks. Mol Biol Evol 18:206–213

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This article was made possible in part by support from a National Institutes of Health grant no. IP20RR18754 from the Institutional Development Award program and National Science Foundation award IOS-0641382.

Author information

Authors and Affiliations

  1. Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA

    Zuly E. Parra & Robert D. Miller

Authors
  1. Zuly E. Parra
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Robert D. Miller
    View author publications

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence to Robert D. Miller.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

Expanded view of the avian TCR Vα/δ groups shown in color in Fig. 2. Keys to the individual sequence numbers are in Supplementary Table 1 (PDF 161 kb)

Supplementary Fig. 2

Alignment of predicted amino acid sequence of avian Vα/δ gene segments. Representative gene segments from the chicken and zebra finch were aligned by group to available sequences from turkey, duck, parrot, and grouse. a Vα1, b Vα2, c Vδ1, and d zebra finch Vδ2 and Vδ4. Conserved cysteine residues involved in intrachain disulfide bonds are highlighted in gray. Alignments were performed as in Fig. 2. Chromosome location: chicken: chr27: a 834130, 791237, 578060, 561959, 524524, 392324, 372896; b 827857, 559594, 445728, 731817, 454878, 469158; c 354411, 339894, 213690, 199617, 184349. Finch: chr27: a 3074837, 3074164, 3068198, 3063816; b 3078066, 3071571, 3065419; c 3054507, 3051702, 3047500; d 3049227, 3033533. GenBank accession numbers: turkey: a ADDD01150225, ADDD01152688; b XM003214154, ADDD01149483, ADDD01151410, ADDD01148254; c ADDD01147795, ADDD01052097. Duck: c AY446069, AY446070, AF323922. Grouse: GW705681. Parrot: a AGAI01024880, AGAI01025999; b AGAI01023412; c AGAI01044297a, AGAI01044297b, AGAI01011509, AGAI01045807, AGAI01030128 (PDF 110 kb)

Supplementary Table 1

GenBank accession numbers of sequences used in Fig. 2 (PDF 49 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Parra, Z.E., Miller, R.D. Comparative analysis of the chicken TCRα/δ locus. Immunogenetics 64, 641–645 (2012). https://doi.org/10.1007/s00251-012-0621-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00251-012-0621-5

Keywords

Profiles

  1. Robert D. Miller View author profile