Abstract
All jawed vertebrates have four T cell receptor (TCR) chains expressed by thymus-derived lymphocytes that play a significant role in animal immune defense. However, avian TCR studies have been limited to a few species, although their co-functional major histocompatibility complexes (MHCs) have been studied for decades, showing various copy numbers and polymorphisms. Here, using public genome data, we characterized the copy numbers, the phylogenic relationship and selection of T cell receptor complex (TCR-C) segments, and the genomic organization of TCR loci across birds. Various numbers of C segments were found in the TCRα/TCRδ, TCRβ, and TCRγ loci, and phylogenetic analysis reflected both ancient gene duplication events (two Cβ segments and Cδ segments divergent into CδI and CδII) and contemporary evolution (lineage-specific and species-specific characteristics). Most passerines lack CδII segments and a second TRD locus, except Meliphagidae and Maluridae. A relatively stable structure was verified in four TCR loci of birds, except for the arrangement of V segment groups. In this study, we explored the phylogenetic relationships of TCR-C segments across avians for the first time. We inferred gene duplication and loss events during the evolution process. The finding of diverse TCR germline repertoires provides a better understanding of the immune systems of birds.
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Data availability
All sequences are available in the public databases.
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Funding
This work was supported by the “Pioneer” and “Leading Goose” R&D Program of Zhejiang (No. 2022C04014), Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding (No. 2021C02068-10), National Natural Science Foundation of China (No. 32101243), and Sichuan and Technology Department of Sichuan Province (Grant No. 2022YFS0487).
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K. H., Y. Z., and A. Z. designed this study; C. L., L. S., Y. Z., and K. H. analyzed the data; C. L. and K. H. wrote the initial draft; all authors revised the draft for intellectual content and approved the final manuscript.
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Highlights
• First large-scale and comprehensive analysis of TCR in birds.
• Ancient gene duplication events in Cβ segments and Cδ segments.
• Provides evidence for loss of a second TRD locus in the CδII fragment in most passerines.
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Liang, C., Sun, L., Zhu, Y. et al. Macroevolution of avian T cell receptor C segments using genomic data. Immunogenetics 75, 531–541 (2023). https://doi.org/10.1007/s00251-023-01322-8
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DOI: https://doi.org/10.1007/s00251-023-01322-8