The Florida Manatee Adaptive Immune Receptor Genes Reveal Novel Patterns in Mammalian Evolution
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The adaptive immune system is responsible for an antigen-specific response that is stronger and faster with each subsequent infection. The hallmarks of this response are the B cell and the T cell, which are responsible for recognizing foreign antigens through their highly diverse receptors: the immunoglobulin (Ig) and T cell receptor (TR). These receptors have been studied in many mammalian species, however there are still gaps in our knowledge throughout mammalian evolution. Two eutherian sister superorders, Afrotheria and Xenarthra, have been neglected in this field of research. Therefore, we chose to characterize the adaptive immune receptor genes of the Florida manatee (Trichechus manatus latirostris), the only afrotherian species that inhabits the United States. We annotated the adaptive immune receptor loci in the genomic scaffolds of the Florida manatee genome and sequenced expressed transcripts using PacBio SMRT sequencing. In the IgH locus, we found limited IgHV diversity. The IgHV segments were limited in number and sequence diversity; the Florida manatee lacked clan III IgHV segments, which are conserved throughout most mammals. The loss of clan III IgHV consistently correlated to a decrease in the number of functional IgHV in cattle, sheep, and horse. This shared phenomenon in an evolutionarily distinct species highlighted the role of the clan III IgHV segments in maintaining locus diversity. Overall, the three TR loci had average to above average diversity. We separated the Florida manatee TRV segments into subgroups based on 75% nucleotide identity and identified conserved subgroups and subgroup order compared to the human TR loci. We identified a direct correlation between locus complexity, TRV sequence conservation, and locus synteny. This revealed the magnitude of overall maintenance of each TR locus across two divergent eutherian mammals for the first time. It also emphasized the role of locus organization on gene evolution. By including this understudied eutherian superorder into the analysis of these complex genes, we identified new evolutionary patterns that help us understand the factors that shaped our immune response.
Breaux, Breanna Laine (2018). The Florida Manatee Adaptive Immune Receptor Genes Reveal Novel Patterns in Mammalian Evolution. Doctoral dissertation, Texas A & M University. Available electronically from