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

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

鸡T细胞受体γ链基因位点重新测序和组装

马俊平^{1, 2}, 杨犀^{1, 2}, 律娜¹, 刘飞¹, 陈燕^{1, 3}, 朱宝利¹

1. 中国科学院微生物研究所,北京 100101;
2. 中国科学院大学,北京 100049;
3. 中国农业科学院北京畜牧兽医研究所ASTIP-IAS03,北京 100193

收稿日期:2014-11-04 修回日期:2015-03-09 出版日期:2015-06-20 发布日期:2015-03-16
通讯作者: 朱宝利,博士,研究员,研究方向：微生物与免疫基因组学。E-mail: zhubaoli@im.ac.cn
陈燕,博士,助理研究员,研究方向：动物遗传育种。E-mail: chenyan0204@163.com
作者简介:马俊平,硕士研究生,专业方向：遗传学和基因组学。E-mail: majp12@im.ac.cn
基金资助:
国家重点基础研究发展规划项目(编号：2015CB554204)资助

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

摘要/Abstract

摘要： 动物T细胞受体(T cell receptor,TCR)基因由多个不同的高度同源的基因家族组成,通过全基因组测序很难获得准确的基因序列和排列位置。文章通过在NCBI中发布的鸡TCR的γ链(TCRγ或TRG)基因片段序列定位了鸡TRG基因所在区域,并确定了与鸡TRG基因位点对应的细菌人工染色体(BAC)克隆(CH261-174P24)。对该克隆进行高通量的重新测序和组装后,得到含有10个scaffolds的基因组草图,较完整地覆盖了鸡TRG基因位点及两侧区域。通过PCR扩增和测序证明了scaffold内部结构的正确性,校正了鸡参考基因组TRG基因位点一个可变基因和一个缺口序列(gap)附近各一处错误序列,以及可变基因区多处序列错误。文章通过校正鸡参考基因组TRG基因位点的序列,为鸡TRA/D和TRB基因位点的基因组序列分析提供了新方法。

关键词: 鸡, T细胞受体(TCR), 伽马链(TCRγ, 或TRG)基因位点, 测序, 组装

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

马俊平, 杨犀, 律娜, 刘飞, 陈燕, 朱宝利. 鸡T细胞受体γ链基因位点重新测序和组装[J]. 遗传, 2015, 37(6): 568-574.

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.

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鸡T细胞受体γ链基因位点重新测序和组装

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

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