BRIEF RESEARCH REPORT article
Front. Immunol.
Sec. Comparative Immunology
This article is part of the Research TopicHerpetological Immunology: Structure, Function, and Disease ImplicationsView all 3 articles
An update on the characterization of immunoglobulin loci in Ambystoma mexicanum
Provisionally accepted
Stephanie Saint Remy Hernández1,2
Diana Laura1,2
E. Ernestina Godoy-Lozano3
Juan Antonio Miguel-Ruiz4
Juan Téllez-Sosa3
Humberto Valdovinos Torres3
Nancy Rivas-Hernández1
Constantinono López-Macías2*
Jesus Martinez-Barnetche3*- 1Instituto Politecnico Nacional Escuela Nacional de Ciencias Biologicas, Mexico City, Mexico
- 2Hospital de Especialidades Centro Medico Nacional Siglo XXI, Mexico City, Mexico
- 3National Institute of Public Health (Mexico), Cuernavaca, Mexico
- 4Departamento de Ciencias Computacionales. Tecnológico Nacional de México/CENIDET Cuernavaca, Morelos, México, Cuernavaca, Morelos, Mexico
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Abstract Background: We previously reported the genomic characterization of immunoglobulin loci in Ambystoma mexicanum of the laboratory d/d white strain, where the IGH locus gene orientation was incompatible with VDJ recombination, suggesting scaffold orientation errors. A novel 29.1 Gbp A. mexicanum genome derived from an F1 cross between A. mexicanum and A. tigrinum (UKY_AmexF1_1) has recently been released, containing only 220 unmapped scaffolds. Here, we present an updated description of the immunoglobulin loci based on this improved genome assembly. Methods: Using our previously annotated AmbMex60DD sequences, we performed an alignment-based annotation followed by manual curation on the UKY_AmexF1_1 assembly. Gene models were further refined using RNA-Seq datasets from axolotl spleen, liver, lung, heart, and gill tissues. Results: The IGH locus was mapped at 350–364 Mbp on chromosome 13q. Synteny is preserved between both genome versions, but in UKY_AmexF1_1, all IGH genes share the same transcriptional orientation. A major difference was observed in the lambda locus, which in the UKY_Amex_F1_1 genome contains 13 IGLC–IGLJ clusters comprising 60 IGLJ genes, compared with only three clusters in the AmbMex60DD genome. No kappa locus was detected in either assembly. Conclusion: This study confirms our previous findings and provides an example of intraspecies structural variation in adaptive immune receptor loci. It underscores the importance of well-assembled genomes and establishes the current A. mexicanum reference as a valuable resource for investigating immune evolution and function in axolotls and other vertebrates.
Keywords: Ambystoma, Comparative genomics, copy number variation, IGH-loci, Immunoglobulin genes
Received: 31 Oct 2025; Accepted: 04 Feb 2026.
Copyright: © 2026 Hernández, Laura, Godoy-Lozano, Miguel-Ruiz, Téllez-Sosa, Torres, Rivas-Hernández, López-Macías and Martinez-Barnetche. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Constantinono López-Macías
Jesus Martinez-Barnetche
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