{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T11:34:16Z","timestamp":1778758456707,"version":"3.51.4"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,9,21]],"date-time":"2021-09-21T00:00:00Z","timestamp":1632182400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,9,21]],"date-time":"2021-09-21T00:00:00Z","timestamp":1632182400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>As one of \u201c\u03b3\u03b4-high\u201d species, chicken is an excellent model for the study of \u03b3\u03b4 T cells in non-mammalian animals. However, a comprehensive characterization of the <jats:italic>TCR\u03b3\u03b4<\/jats:italic> repertoire is still missing in chicken. The objective of this study was to characterize the expressed <jats:italic>TCR\u03b3<\/jats:italic> repertoire in chicken thymus using high-throughput sequencing.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>In this study, we first obtained the detailed genomic organization of the <jats:italic>TCR\u03b3<\/jats:italic> locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the <jats:italic>TCR\u03b3<\/jats:italic> repertoire in the thymus of four chickens by using 5\u2032 Rapid Amplification of cDNA Ends (5\u2032 RACE) along with high-throughput sequencing (HTS).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The chicken <jats:italic>TCR\u03b3<\/jats:italic> locus contains a single C\u03b3 gene, three functional J\u03b3 segments and 44 V\u03b3 segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken <jats:italic>TCR\u03b3<\/jats:italic> locus against itself showed that almost all the entire zone containing V\u03b3 segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 V\u03b3 gene segments, has tandemly duplicated for four times. For the analysis of chicken <jats:italic>TCR\u03b3<\/jats:italic> repertoire, more than 100,000 unique V\u03b3-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline V\u03b3 and J\u03b3 segments identified above, we found that the four chickens had similar repertoire profile of <jats:italic>TCR\u03b3<\/jats:italic>. In brief, four V\u03b3 segments (including V\u03b33.7, V\u03b32.13, V\u03b31.6 and V\u03b31.3) and six V\u03b3-J\u03b3 pairs (including V\u03b33.7-J\u03b33, V\u03b32.13-J\u03b31, V\u03b32.13-J\u03b33, V\u03b31.6-J\u03b33, V\u03b33.7-J\u03b31 and V\u03b31.6-J\u03b31) were preferentially utilized by all four individuals, and vast majority of the unique CDR3\u03b3 sequences encoded 4 to 22 amino acids with mean 12.90 amino acids, which exhibits a wider length distribution and\/or a longer mean length than CDR3\u03b3 of human, mice and other animal species.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>In this study, we present the first in-depth characterization of the <jats:italic>TCR\u03b3<\/jats:italic> repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07975-7","type":"journal-article","created":{"date-parts":[[2021,9,21]],"date-time":"2021-09-21T16:08:03Z","timestamp":1632240483000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Characterization of the chicken T cell receptor \u03b3 repertoire by high-throughput sequencing"],"prefix":"10.1186","volume":"22","author":[{"given":"Tongtong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qian","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqing","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Kang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunliang","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,9,21]]},"reference":[{"key":"7975_CR1","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nature23091","volume":"547","author":"ST Reddy","year":"2017","unstructured":"Reddy ST. 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