Tandem TRA/TRD loci expand TCRα/δ recombination topology in crocodilians

Crocodilians retain an unusual tandem organization of two classical TRA/TRD composite loci, but whether this architecture alters receptor recombination has been unclear. Here, chromosome-level annotation of Chinese alligator ( Alligator sinensis ) and American alligator ( Alligator mississippiensis ) TR loci, integrated with recombination signal sequence (RSS) analysis and RNA-seq-derived repertoire reconstruction, shows that both TRA/TRD modules are transcriptionally productive and functionally connected. In Alligator sinensis , 30.6% of classified TRA rearrangements joined a V segment from one module to a J segment in the other. For TRD , 33.0% followed a cross-locus V-D route followed by local D-J joining. RSS orientation supports deletional recombination across the co-oriented tandem loci, whereas C-region association remains local through RNA splicing. These findings identify spatial connectivity between duplicated antigen-receptor modules as an additional layer of TCR diversity generation in crocodilians.