The Florida manatee ( Trichechus manatus latirostris ) T cell receptor loci exhibit V segment locus synteny and chain-specific evolution
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AbstractManatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent order Afrotheria. We have previously described the immunoglobulin heavy chain locus of the Florida manatee (Trichechus manatus latirostris) and found limited antigen receptor diversity in this humoral arm of the adaptive immune system. We therefore investigated the antigen receptor loci of the cellular arm: the T cell receptor. Manatees are the first species from either Afrotheria or Xenarthra, the most basal eutherian taxonomic groups, to have an in-depth characterization of all T cell receptor loci and expressed repertoires. We manually annotated the three TR loci on the T. m. latirostris genomic scaffolds using BLAST and RSSsite, and compared the segments and overall genomic organization to the human TR loci. We identified the human V segment subgroups that are conserved in T. m. latirostris and found that TRADV are most conserved, TRBV are moderately conserved, and TRGV are the least conserved. The V segment order in the TRAD and TRB loci also showed synteny between the two species. The TRAD locus had five V segment subgroup synteny blocks that showed long-range duplications in the T. m. latirostris locus. The TRB locus had three V segment subgroup synteny blocks that showed short-range duplications. The conservation of V segment sequence and order correlated to the locus complexity, emphasizing the role of genomic organization on gene evolution. We also identified evidence for a VH pseudogene for the first time in a eutherian mammal. These novel findings underline the value of including species within the basal radiation of eutherian evolution in comparative studies.
