# An update on the characterization of immunoglobulin loci in Ambystoma mexicanum

## TL;DR

This study updates the characterization of immunoglobulin loci in axolotls using a new genome assembly, revealing structural differences in immune gene clusters.

## Contribution

The study provides an updated and corrected characterization of immunoglobulin loci in A. mexicanum using a new genome assembly.

## Key findings

- The IGH locus in the new genome assembly has genes in the same transcriptional orientation, resolving previous inconsistencies.
- The lambda locus in the new assembly contains 13 IGLC–IGLJ clusters with 60 IGLJ genes, compared to only three clusters in the older assembly.
- No kappa locus was detected in either genome assembly, confirming prior observations.

## Abstract

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.

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.

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.

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.