[Re-sequencing and assembly of chicken T cell receptor gamma locus].
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.
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;University of Chinese Academy of Sciences, Beijing 100049, China;
Jun-ping
JP
Ma
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China;
Xi
X
Yang
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Na
N
Lv
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Fei
F
Liu
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, ASTIP-IAS03, Beijing 100193, China;
Yan
Y
Chen
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Bao-li
BL
Zhu
D000818:Animals; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D019675:Genes, T-Cell Receptor gamma; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA