Turtle IgD2 preserves an ancestral IgXA-derived XA3-XA4 module in a duplicated and locally remodeled IgD2-IgY constant-region2 array

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 IgD2 architectures have subsequently been recognized in turtles and crocodilians. Here we analyzed Testudines constant-region annotations to determine whether turtle IgD2 represents an intact ancient paralogue or a locally remodeled mosaic gene. Across representative turtle genomes, mixed loci frequently contained upstream D1-D4 exons followed by 3_XA and 4_XA. A direct comparison of paired turtle XA3-XA4 modules with amphibian IgXA and IgM references showed that all turtle modules were closer to amphibian IgXA than to either amphibian or turtle IgM. Upstream D exons, especially D1-D3, instead showed strong local similarity to canonical IgD exons within the same species. A conservative nucleotide tract-permutation test confirmed clustered conversion-like tracts in a subset of D1 and D2 exons, whereas D3 retained local affinity without significant tract clustering. IgY analysis identified 76 complete Y1-Y4 blocks; most were genomically proximal to XA-bearing IgD2 loci on the opposite strand, and contig-restricted randomization confirmed that this association was non-random. All six amino-acid distance-matrix comparisons among Y1-Y4 were significantly correlated, supporting a coupled IgY history without a D-like domain-specific rupture. Independent reannotation recovered 13 complete, one-to-one IgD2/XA-IgY pairs in Chelonia mydas; a thymus transcript encoded the complete D1-D4/XA3- XA4 architecture. Dermochelys coriacea provided three further complete pairs. In Mauremys reevesii, 14 oppositely oriented modules form an array marked by segmental duplication, strand switches, and exon loss. These results support an ancestral paired IgD2-IgY architecture that expanded by segmental duplication to generate the present germline array, while a subset of IgD2 D1 and D2 exons continued to undergo recent intra-species exchange with canonical IgD-derived material. The genomic mechanism can be reconstructed, but the biological significance of maintaining this unusual opposite-strand association remains unknown.