Qualitative and quantitative description of the TCRß repertoire in bank vole (Myodes glareolus)

In the present study, we have adapted protocols available for human and mouse to perform the first in-depth characterization of a TCRß repertoire in a non-model specie. We took advantage of the fact that RACE technique is able to amplify the CDR3 region from TCRs in the species of interest without prior knowledge of neighboring V segments. Necessary primers within the constant region of the TCRß were designed based on de novo assembled transcriptomes, approach successfully tested before in the highly complex MHC gene family (Migalska et al. 2016). RACE products of the TCRß chains from seven bank voles covered the full CDR3 sequences, as well as entire V and J segments. Detailed qualitative analysis involved the V and J segment description, as well as revealed CDR3 length distribution and V/J segment usage. Modified protocol incorporating UMIs enabled quantitative analysis and was performed for additional three individuals, including an estimation of TCR repertoire size and a comparison of the common vs. private TCRß repertoires.