Gambon Deza, F.

A second IgD gene, IgD2, was first described in the leopard gecko as a hybrid constant-region gene containing IgD-derived exons and terminal IgA-like exons. Related architectures have subsequently been identified in turtles and crocodilians. Here, we analyzed Testudines immunoglobulin heavy-chain constant-region loci to determine whether turtle IgD2 represents an intact ancient paralogue or a locally remodeled mosaic gene. Across turtle genomes, IgD2 loci commonly contained D1-D4 exons followed by XA3 and XA4. Comparisons with amphibian IgXA and IgM showed that turtle XA3-XA4 modules are consistently closer to amphibian IgXA than to IgM, supporting their origin from the ancestral IgXA described in amphibians. In contrast, the upstream D exons, particularly D1-D3, showed strong local similarity to canonical IgD exons from the same species. Nucleotide tract-permutation tests identified conversion-like tracts in a subset of D1 and D2 exons, whereas D3 retained local affinity without significant tract clustering. We identified 76 complete IgY genes, most located close to XA-bearing IgD2 genes on the opposite strand. All six comparisons among Y1-Y4 amino-acid distance matrices were significantly correlated, supporting a coupled IgY evolutionary history without the domain-specific disruption observed in IgD2. Independent genome analyses recovered 13 complete IgD2/XA-IgY pairs in Chelonia mydas, three in Dermochelys coriacea, and an expanded array of 14 modules in Mauremys reevesii. Genomic self-alignments demonstrated segmental duplication of complete paired units, followed in some lineages by inversion and exon loss. A Chelonia mydas thymus transcript independently confirmed expression of the complete D1-D4-XA3-XA4 architecture. These results support an ancestral paired IgD2-IgY organization that expanded through segmental duplication, while some IgD2 D1 and D2 exons continued to undergo recent intra-species exchange with canonical IgD-derived material. The genomic mechanism is supported, but the biological significance of maintaining this unusual opposite-strand association remains unknown.