鸡T细胞受体γ链基因位点重新测序和组装

doi:10.16288/j.yczz.14-382

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HEREDITAS(Beijing) ›› 2015, Vol. 37 ›› Issue (6): 568-574.doi: 10.16288/j.yczz.14-382

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Re-sequencing and assembly of chicken T cell receptor gamma locus

Junping Ma^{1, 2}, Xi Yang^{1, 2}, Na Lv¹, Fei Liu¹, Yan Chen^{1, 3}, Baoli Zhu¹

1. Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
2. University of Chinese Academy of Sciences, Beijing 100049, China;
3. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, ASTIP-IAS03, Beijing 100193, China

Received:2014-11-04 Revised:2015-03-09 Online:2015-06-20 Published:2015-03-16

Abstract

Abstract: The genomic organization of the animal T cell receptor (TCR) loci is characterized by different gene families with high homology, and it is quite difficult to obtain accurate gene sequences and arrangements of these gene families. In this study, we identified the location of chicken TCR gamma chain (TCRγ or TRG) genes by comparing those TRG gene sequences with the chicken reference genome, and the corresponding bacterial artificial chromosome (BAC) clone, CH261-174P24, was chosen for further high-throughput DNA re-sequencing and assembly. As a result, a draft genome assembly containing ten scaffolds was obtained, which almost covered the chicken TRG gene locus and the flanking regions. Subsequently, the internal structure of these scaffolds was confirmed by PCR amplification and Sanger sequencing. Our analysis corrected two errors in the sequence—one near a TRG variable gene and one close to a gap, respectively, and several errors in the TRG variable genes in the chicken reference genome. In conclusion, our work has partially corrected the erroneously assembled sequences of the TRG gene locus in the chicken reference genome and thus provides a new method for genome sequence analysis of chicken TRA/D and TRB gene loci.

Key words: chicken, T cell receptor (TCR), gamma gene locus, re-sequencing, assembling

Junping Ma, Xi Yang, Na Lv, Fei Liu, Yan Chen, Baoli Zhu. Re-sequencing and assembly of chicken T cell receptor gamma locus[J]. HEREDITAS(Beijing), 2015, 37(6): 568-574.

References

[1] Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AFA, Wang K, Koop BF, Hood L. Comparative genomics of the human and mouse T cell receptor loci. Immunity , 2001, 15(3): 337-349.
[2] Clark SP, Arden B, Kabelitz D, Mak TW. Comparison of human and mouse T-cell receptor variable gene segment subfamilies. Immunogenetics , 1995, 42(6): 531-540.
[3] Mackelprang R, Carlson CS, Subrahmanyan L, Livingston RJ, Eberle MA, Nickerson DA. Sequence variation in the human T-cell receptor loci. Immunol Rev , 2002, 190(1): 26-39.
[4] 李扬秋. T细胞受体的研究和应用. 北京: 人民卫生出版社, 2009: 53-55.
[5] Chen CL, Ager LL, Gartland GL, Cooper MD. Identification of a T3/T cell receptor complex in chickens. J Exp Med , 1986, 164(1): 375-380.
[6] Sowder JT, Chen CL, Ager LL, Chan MM, Cooper MD. A large subpopulation of avian T cells express a homologue of the mammalian T gamma/delta receptor. J Exp Med , 1988, 167(2): 315-322.
[7] Vainio O, Lassila O, Cihak J, Lösch U, Houssaint E. Tissue distribution and appearance in ontogeny of α/β T cell receptor (TCR2) in chicken. Cell Immunol , 1990, 125(1): 254-260.
[8] Tjoelker LW, Carlson LM, Lee K, Lahti J, McCormack WT, Leiden JM, Chen CL, Cooper MD, Thompson CB. Evolutionary conservation of antigen recognition: the chicken T-cell receptor beta chain. Proc Natl Acad Sci USA , 1990, 87(20): 7856-7860.
[9] McCormack WT, Tjoelker LW, Stella G, Postema CE, Thompson CB. Chicken T-cell receptor beta-chain diversity: an evolutionarily conserved D beta-encoded glycine turn within the hypervariable CDR3 domain. Proc Natl Acad Sci USA , 1991, 88(17): 7699-7703.
[10] Cihak J, Hoffmann-Fezer G, Ziegler-Heibrock HW, Stein H, Kaspers B, Chen CH, Cooper MD, Lösch U. T cells expressing the V beta 1 T-cell receptor are required for IgA production in the chicken. Proc Natl Acad Sci USA , 1991, 88(23): 10951-10955.
[11] Göbel TW, Chen CL, Lahti J, Kubota T, Kuo CL, Aebersold R, Hood L, Cooper MD. Identification of T-cell receptor alpha-chain genes in the chicken. Proc Natl Acad Sci USA , 1994, 91(3): 1094-1098.
[12] Six A, Rast JP, McCormack WT, Dunon D, Courtois D, Li Y, Chen CH, Cooper MD. Characterization of avian T-cell receptor γgenes. Proc Natl Acad Sci USA , 1996, 93(26): 15329-15334.
[13] Kubota T, Wang JY, Göbel TWF, Hockett RD, Cooper MD, Chen CH. Characterization of an avian (Gallus gallus domesticus) TCR αδ gene locus. J Immunol , 1999, 163(7): 3858-3866.
[14] International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature , 2004, 432(7018): 695-716.
[15] Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao FQ, Zhu BL. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC Bioinformatics , 2013, 14: 33.
[16] Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res, 2009, 19(6): 1117-1123.
[17] Bonfield JK, Staden R. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res , 1995, 23(8): 1406-1410.
[18] Tillinghast JP, Behlke MA, Loh DY. Structure and diversity of the human T-cell receptor beta-chain variable region genes. Science , 1986, 233(4766): 879-883.
[19] Rowen L, Koop BF, Hood L. The complete 685-kilobase DNA sequence of the human β T cell receptor locus. Science , 1996, 272(5269): 1755-1762.
[20] Ikuta K, Ogura T, Shimizu A, Honjo T. A joining-diversity- joining complex generated by inversion mechanism and a variable-diversity complex in the β-chain gene of the human T-cell receptor. Nucl Acids Res , 1986, 14(12): 4899-4909.
[21] Tunnacliffe A, Kefford R, Milstein C, Forster A, Rabbitts TH. Sequence and evolution of the human T-cell antigen receptor beta-chain genes. Proc N

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Re-sequencing and assembly of chicken T cell receptor gamma locus

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