{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T17:04:45Z","timestamp":1794330285952,"version":"4.9.0"},"reference-count":87,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T00:00:00Z","timestamp":1759190400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Amphibians are valuable models for comparative immunology. In the caudate <jats:italic>Ambystoma mexicanum<\/jats:italic>, the architecture of immunoglobulin loci resembles that of the anuran <jats:italic>Xenopus tropicalis<\/jats:italic>, although some antibody gene features are absent. Evidence supports the presence of T lymphocytes in axolotl, the expression of T cell receptor alpha, beta, and delta chains, and a restricted diversity in the delta chain. Here, we describe the T cell receptor loci in the <jats:italic>A. mexicanum<\/jats:italic> genome and compare them with <jats:italic>X. tropicalis<\/jats:italic> and other tetrapods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>T cell receptor loci were mapped and annotated in the <jats:italic>A. mexicanum<\/jats:italic> genome (UKY_AMEXF1_1) using reference sequences from axolotl, <jats:italic>X. tropicalis<\/jats:italic>, human, and mouse. Gene models were refined with RNA sequencing data from spleen, lung, and liver.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The T cell receptor alpha and delta locus in axolotl shows an overall conserved structure compared with other tetrapods. The alpha locus contained a higher number of variable genes than the beta and delta loci, with a predominance of functional genes (ratio 3.06). No gene encoding the pre-T cell receptor chain alpha was identified. The delta locus harbored two conventional variable genes, but no expression was detected in RNA sequencing data, suggesting pseudogenization. Neither delta chain diversity genes nor gamma chain elements were found in the genome or spleen transcriptome. The beta locus displayed structural similarity to that of other tetrapods and included five translocons with diversity, joining, and constant segments. One constant gene consisted of two exons encoding two constant domains. Functional variable genes predominated in the beta locus (ratio 3.6).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our study reveals conserved but distinctive features of axolotl T cell receptor loci, including restricted delta-chain diversity, absence of gamma chain and pre-T cell receptor alpha, and structural novelty in the beta locus. These findings provide new insights into the evolution of T cell receptors in amphibians and offer a genomic framework to explore the links between adaptive immunity and tissue regeneration in <jats:italic>A. mexicanum<\/jats:italic>.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2025.1656386","type":"journal-article","created":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:12:15Z","timestamp":1759205535000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Genomic characterization of the T-cell receptor loci in Ambystoma mexicanum"],"prefix":"10.3389","volume":"16","author":[{"given":"Diana L.","family":"Pacheco-Olvera","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Saint Remy-Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Ernestina","family":"Godoy-Lozano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"T\u00e9llez-Sosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Humberto","family":"Valdovinos-Torres","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Everado","family":"Curiel-Quesada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Constantino","family":"L\u00f3pez-Mac\u00edas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesus","family":"Mart\u00ednez-Barnetche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1038\/nri2807","article-title":"The origins of vertebrate adaptive immunity","volume":"10","author":"Litman","year":"2010","journal-title":"Nat Rev Immunol"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.01.007","article-title":"Mechanisms of programmed DNA lesions and genomic instability in the immune system","volume":"152","author":"Alt","year":"2013","journal-title":"Cell"},{"key":"B3","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-20819-0_11","article-title":"The Evolution and Structure of Atypical T Cell Receptors","volume-title":"Pathogen-Host Interactions: Antigenic Variation v Somatic Adaptations","author":"Hansen","year":"2015"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2006.01.006","article-title":"Deconstructing the form and function of the TCR\/CD3 complex","volume":"24","author":"Kuhns","year":"2006","journal-title":"Immunity"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2014.09.004","article-title":"Characterizing immune repertoires by high throughput sequencing: strategies and applications","volume":"35","author":"Calis","year":"2014","journal-title":"Trends Immunol"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201040515","article-title":"The dynamic TCR\u03b4: TCR\u03b4 chains in the amphibian Xenopus tropicalis utilize antibody-like V genes","volume":"40","author":"Parra","year":"2010","journal-title":"Eur J Immunol"},{"key":"B7","doi-asserted-by":"publisher","first-page":"544","DOI":"10.3390\/genes12040544","article-title":"The genomic organisation of the TRA\/TRD locus validates the peculiar characteristics of dromedary \u03b4-chain expression","volume":"12","author":"Massari","year":"2021","journal-title":"Genes (Basel)"},{"key":"B8","doi-asserted-by":"publisher","first-page":"381","DOI":"10.3390\/biom12030381","article-title":"IMGT\u00aeHomo sapiens IG and TR loci, gene order, CNV and haplotypes: New concepts as a paradigm for jawed vertebrates genome assemblies","volume":"12","author":"Lefranc","year":"2022","journal-title":"Biomolecules"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.2000257","article-title":"Analysis of the Chinese alligator TCR\u03b1\/\u03b4 Loci reveals the evolutionary pattern of atypical TCR\u03b4\/TCR\u03bc in tetrapods","volume":"205","author":"Wang","year":"2020","journal-title":"J Immunol"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-012-0621-5","article-title":"Comparative analysis of the chicken TCR\u03b1\/\u03b4 locus","volume":"64","author":"Parra","year":"2012","journal-title":"Immunogenetics"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-016-0904-3","article-title":"Genomic organization of the zebrafish (Danio rerio) T cell receptor alpha\/delta locus and analysis of expressed products","volume":"68","author":"Seelye","year":"2016","journal-title":"Immunogenetics"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.immunol.17.1.109","article-title":"Evolution of antigen binding receptors","volume":"17","author":"Litman","year":"1999","journal-title":"Annu Rev Immunol"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0507074103","article-title":"An evolutionarily mobile antigen receptor variable region gene: doubly rearranging NAR-TcR genes in sharks","volume":"103","author":"Criscitiello","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B14","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/1471-2164-9-111","article-title":"Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica","volume":"9","author":"Parra","year":"2008","journal-title":"BMC Genomics"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1103521","article-title":"A second TCR\u03b4 locus in Galliformes uses antibody-like V domains: insight into the evolution of TCR\u03b4 and TCR\u03bc genes in tetrapods","volume":"188","author":"Parra","year":"2012","journal-title":"J Immunol"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss128","article-title":"A model for the evolution of the mammalian t-cell receptor \u03b1\/\u03b4 and \u03bc loci based on evidence from the duckbill Platypus","volume":"29","author":"Parra","year":"2012","journal-title":"Mol Biol Evol"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/6.7.657","article-title":"Emergence of the immunoglobulin family: conservation in protein sequence and plasticity in gene organization","volume":"6","author":"Marchalonis","year":"1996","journal-title":"Glycobiology"},{"key":"B18","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1111\/j.1600-065X.1998.tb01255.x","article-title":"T-cell receptors in ectothermic vertebrates","volume":"166","author":"Charlemagne","year":"1998","journal-title":"Immunol Rev"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/nri1712","article-title":"Reconstructing immune phylogeny: new perspectives","volume":"5","author":"Litman","year":"2005","journal-title":"Nat Rev Immunol"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1002\/dvdy.21891","article-title":"Comparative and developmental study of the immune system in Xenopus","volume":"238","author":"Robert","year":"2009","journal-title":"Dev Dyn"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.iy.07.040189.001343","article-title":"The immune system of Xenopus","volume":"7","author":"Du Pasquier","year":"1989","journal-title":"Annu Rev Immunol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1093\/biosci\/biv153","article-title":"A tale of two axolotls","volume":"65","author":"Voss","year":"2015","journal-title":"Bioscience"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1038\/nature25458","article-title":"The axolotl genome and the evolution of key tissue formation regulators","volume":"554","author":"Nowoshilow","year":"2018","journal-title":"Nature"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1039274","article-title":"Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum","volume":"14","author":"Martinez-Barnetche","year":"2023","journal-title":"Front Immunol"},{"key":"B25","article-title":"Thymus independent anti-horse erythrocyte antibody response and suppressor T cells in the Mexican axolotl (Amphibia, Urodela, ambystoma mexicanum)","volume":"36","author":"Charlemagne","year":"1979","journal-title":"Immunology"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1007\/s002510050198","article-title":"Structure and diversity of the T-cell receptor alpha chain in the Mexican axolotl","volume":"45","author":"Fellah","year":"1997","journal-title":"Immunogenetics"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1002\/1521-4141(200205)32:5<1349::AID-IMMU1349>3.0.CO;2-X","article-title":"Structure, diversity and expression of the TCRdelta chains in the Mexican axolotl","volume":"32","author":"Fellah","year":"2002","journal-title":"Eur J Immunol"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1002\/eji.200636375","article-title":"Highly restricted diversity of TCR delta chains of the amphibian Mexican axolotl (Ambystoma mexicanum) in peripheral tissues","volume":"37","author":"Andr\u00e9","year":"2007","journal-title":"Eur J Immunol"},{"key":"B29","doi-asserted-by":"publisher","first-page":"e2017176118","DOI":"10.1073\/pnas.2017176118","article-title":"The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci","volume":"118","author":"Schloissnig","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-002-0474-4","article-title":"Structure and diversity of T-lymphocyte antigen receptors alpha and gamma in Xenopus","volume":"54","author":"Haire","year":"2002","journal-title":"Immunogenetics"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.163.7.3858","article-title":"Characterization of an avian (Gallus gallus domesticus) TCR alpha delta gene locus","volume":"163","author":"Kubota","year":"1999","journal-title":"J Immunol"},{"key":"B32","doi-asserted-by":"publisher","first-page":"624","DOI":"10.3390\/genes11060624","article-title":"Evolution of the T-cell receptor (TR) loci in the adaptive immune response: the tale of the TRG locus in mammals","volume":"11","author":"Antonacci","year":"2020","journal-title":"Genes"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-021-00628-6","article-title":"Structural insights into the evolution of the RAG recombinase","volume":"22","author":"Liu","year":"2022","journal-title":"Nat Rev Immunol"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2009.03.018","article-title":"Antigen ligation triggers a conformational change within the constant domain of the alphabeta T cell receptor","volume":"30","author":"Beddoe","year":"2009","journal-title":"Immunity"},{"key":"B35","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1016\/j.immuni.2018.09.007","article-title":"The T cell antigen receptor \u03b1 transmembrane domain coordinates triggering through regulation of bilayer immersion and CD3 subunit associations","volume":"49","author":"Brazin","year":"2018","journal-title":"Immunity"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1016\/s1074-7613(00)80500-2","article-title":"A motif within the T cell receptor alpha chain constant region connecting peptide domain controls antigen responsiveness","volume":"5","author":"B\u00e4ckstr\u00f6m","year":"1996","journal-title":"Immunity"},{"key":"B37","first-page":"397","volume-title":"The T Cell Receptor FactsBook","author":"Lefranc","year":"2001"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00821","article-title":"IMGT\u00ae biocuration and comparative study of the T cell receptor beta locus of veterinary species based on Homo sapiens TRB","volume":"11","author":"P\u00e9gorier","year":"2020","journal-title":"Front Immunol"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1238321","article-title":"Evolution of T cell receptor beta loci in salmonids","volume":"14","author":"Boudinot","year":"2023","journal-title":"Front Immunol"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1000732","article-title":"Distinctive CD3 heterodimeric ectodomain topologies maximize antigen-triggered activation of alpha beta T cell receptors","volume":"185","author":"Kim","year":"2010","journal-title":"J Immunol"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.67195","article-title":"Structural variability and concerted motions of the T cell receptor - CD3 complex","volume":"10","author":"Pandey","year":"2021","journal-title":"Elife"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-7613(01)00200-X","article-title":"Comparative genomics of the human and mouse T cell receptor loci","volume":"15","author":"Glusman","year":"2001","journal-title":"Immunity"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1010166107","article-title":"Identification of the pre-T-cell receptor alpha chain in nonmammalian vertebrates challenges the structure-function of the molecule","volume":"107","author":"Smelty","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1038\/327677a0","article-title":"A new T-cell receptor gene located within the alpha locus and expressed early in T-cell differentiation","volume":"327","author":"Chien","year":"1987","journal-title":"Nature"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.21.8166","article-title":"Genomic organization of the human T-cell antigen-receptor alpha\/delta locus","volume":"85","author":"Satyanarayana","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B46","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1186\/1471-2164-15-994","article-title":"Genomic analysis offers insights into the evolution of the bovine TRA\/TRD locus","volume":"15","author":"Connelley","year":"2014","journal-title":"BMC Genomics"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S1074-7613(00)80237-X","article-title":"alpha, beta, gamma, and delta T cell antigen receptor genes arose early in vertebrate phylogeny","volume":"6","author":"Rast","year":"1997","journal-title":"Immunity"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1002\/jez.b.22558","article-title":"Genome complexity in the coelacanth is reflected in its adaptive immune system","volume":"322","author":"Saha","year":"2014","journal-title":"J Exp Zool B Mol Dev Evol"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(17)49904-2","article-title":"The structural basis of T-cell receptor (TCR) activation: An enduring enigma","volume":"295","author":"Mariuzza","year":"2020","journal-title":"J Biol Chem"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2015.00441","article-title":"Structural features of the \u03b1\u03b2TCR mechanotransduction apparatus that promote pMHC discrimination","volume":"6","author":"Brazin","year":"2015","journal-title":"Front Immunol"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1038\/nri2941","article-title":"Recombination centres and the orchestration of V(D)J recombination","volume":"11","author":"Schatz","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1097\/HS9.0000000000000948","article-title":"Dominant T-cell receptor delta rearrangements in B-cell precursor acute lymphoblastic leukemia: Leukemic markers or physiological \u03b3\u03b4 T repertoire","volume":"7","author":"Kelm","year":"2023","journal-title":"HemaSphere"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.0902774","article-title":"Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark","volume":"184","author":"Criscitiello","year":"2010","journal-title":"J Immunol"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1126\/science.abe7070","article-title":"The molecular assembly of the marsupial \u03b3\u03bc T cell receptor defines a third T cell lineage","volume":"371","author":"Morrissey","year":"2021","journal-title":"Science"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.2101158","article-title":"Comparison of reptilian genomes reveals deletions associated with the natural loss of \u03b3\u03b4 T cells in squamates","volume":"208","author":"Morrissey","year":"2022","journal-title":"J Immunol"},{"key":"B56","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1146\/annurev-immunol-102819-023144","article-title":"The innate biologies of adaptive antigen receptors","volume":"38","author":"Hayday","year":"2020","journal-title":"Annu Rev Immunol"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.153.10.4539","article-title":"Evolution of T cell receptor genes. Extensive diversity of V beta families in the Mexican axolotl","volume":"153","author":"Fellah","year":"1994","journal-title":"J Immunol"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1007\/s002510050124","article-title":"The structure, rearrangement, and ontogenic expression of DB and JB gene segments of the Mexican axolotl T-cell antigen receptor beta chain (TCRB)","volume":"44","author":"Kerfourn","year":"1996","journal-title":"Immunogenetics"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1002\/1521-4141(200102)31:2<403::AID-IMMU403>3.0.CO;2-4","article-title":"Complexity of the T cell receptor Cbeta isotypes in the Mexican axolotl: structure and diversity of the VDJCbeta3 and VDJCbeta4 chains","volume":"31","author":"Fellah","year":"2001","journal-title":"Eur J Immunol"},{"key":"B60","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/BF00768834","article-title":"Human lambda light chain locus: organization and DNA sequences of three genomic J regions","volume":"25","author":"Udey","year":"1987","journal-title":"Immunogenetics"},{"key":"B61","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1016\/j.molimm.2007.05.023","article-title":"Organization, structure and evolution of 41kb of genomic DNA spanning the D-J-C region of the sheep TRB locus","volume":"45","author":"Antonacci","year":"2008","journal-title":"Mol Immunol"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-013-0754-1","article-title":"Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses","volume":"66","author":"Antonacci","year":"2014","journal-title":"Immunogenetics"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20020119","article-title":"Involvement of the TCR Cbeta FG loop in thymic selection and T cell function","volume":"195","author":"Sasada","year":"2002","journal-title":"J Exp Med"},{"key":"B64","doi-asserted-by":"publisher","DOI":"10.1101\/gr.241901.118","article-title":"A chromosome-scale assembly of the axolotl genome","volume":"29","author":"Smith","year":"2019","journal-title":"Genome Res"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1002\/dvdy.257","article-title":"Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum)","volume":"250","author":"Timoshevskaya","year":"2021","journal-title":"Dev Dyn"},{"key":"B66","doi-asserted-by":"publisher","DOI":"10.1016\/j.it.2017.04.003","article-title":"The individual and population genetics of antibody immunity","volume":"38","author":"Watson","year":"2017","journal-title":"Trends Immunol"},{"key":"B67","doi-asserted-by":"publisher","first-page":"888","DOI":"10.1111\/imcb.12288","article-title":"A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains","volume":"97","author":"Watson","year":"2019","journal-title":"Immunol Cell Biol"},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2020.12.018","article-title":"Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles","volume":"54","author":"V\u00e1zquez Bernat","year":"2021","journal-title":"Immunity"},{"key":"B69","doi-asserted-by":"publisher","first-page":"33","DOI":"10.4049\/immunohorizons.1900095","article-title":"The genome resequencing of TCR loci in Gallus gallus revealed their distinct evolutionary features in avians","volume":"4","author":"Liu","year":"2020","journal-title":"ImmunoHorizons"},{"key":"B70","first-page":"389","volume-title":"The origins of genome architecture","author":"Lynch","year":"2007"},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.5808\/GI.2015.13.4.112","article-title":"Introns: The functional benefits of introns in genomes","volume":"13","author":"Jo","year":"2015","journal-title":"Genomics Inform"},{"key":"B72","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/sj.hdy.6801059","article-title":"The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations","volume":"100","author":"Comeron","year":"2008","journal-title":"Heredity (Edinb)"},{"key":"B73","doi-asserted-by":"publisher","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.1038\/322379a0","article-title":"Alternative splicing of murine TCR beta transcripts","volume":"322","author":"Behlke","year":"1986","journal-title":"Nature"},{"key":"B75","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.15.7799","article-title":"Evolution by the birth-and-death process in multigene families of the vertebrate immune system","volume":"94","author":"Nei","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.1038\/nri1636","article-title":"Unique features of the pre-T-cell receptor alpha-chain: not just a surrogate","volume":"5","author":"von Boehmer","year":"2005","journal-title":"Nat Rev Immunol"},{"key":"B77","article-title":"A role for effectors of cellular immunity in epimorphic regeneration of amphibian limbs","volume":"16","author":"Fahmy","year":"2002","journal-title":"In Vivo"},{"key":"B78","doi-asserted-by":"publisher","first-page":"5153","DOI":"10.1038\/s41467-018-07604-0","article-title":"Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution","volume":"9","author":"Leigh","year":"2018","journal-title":"Nat Commun"},{"key":"B79","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/j.devcel.2017.11.010","article-title":"Zebrafish regulatory T cells mediate organ-specific regenerative programs","volume":"43","author":"Hui","year":"2017","journal-title":"Dev Cell"},{"key":"B80","doi-asserted-by":"publisher","DOI":"10.1016\/j.acthis.2011.07.001","article-title":"The thymus and tail regenerative capacity in Xenopus laevis tadpoles","volume":"114","author":"Franchini","year":"2012","journal-title":"Acta Histochem"},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.1002\/dvdy.251","article-title":"Immunity in salamander regeneration: Where are we standing and where are we headed","volume":"250","author":"Bola\u00f1os-Castro","year":"2021","journal-title":"Dev Dyn"},{"key":"B82","unstructured":"mbystoma mexicanum genome assembly UKY_AmexF1_1\n          \n          \n          \n          2025"},{"key":"B83","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Briefings Bioinf"},{"key":"B85","article-title":"T-cell receptor and immunoglobulin nomenclature sub-committee","year":"2023"},{"key":"B86","doi-asserted-by":"publisher","first-page":"595","DOI":"10.1101\/pdb.top115","article-title":"IMGT, the international imMunoGeneTics information system","volume":"2011","author":"Lefranc","year":"2011","journal-title":"Cold Spring Harb Protoc"},{"key":"B87","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PloS Comput Biol"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1656386\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T12:35:49Z","timestamp":1759408549000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1656386\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,30]]},"references-count":87,"alternative-id":["10.3389\/fimmu.2025.1656386"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386","relation":{"has-part":[{"id-type":"doi","id":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386.s001","asserted-by":"subject"},{"id-type":"doi","id":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386.s002","asserted-by":"subject"},{"id-type":"doi","id":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386.s003","asserted-by":"subject"},{"id-type":"doi","id":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386.s004","asserted-by":"subject"},{"id-type":"doi","id":"https:\/\/doi.org\/10.3389\/fimmu.2025.1656386.s005","asserted-by":"subject"}]},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,30]]},"article-number":"1656386"}}