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. 2021 Oct 18;12:753960. doi: 10.3389/fimmu.2021.753960

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Copyright © 2021 Edholm, Fenton, Mondot, Paulssen, Lefranc, Boudinot and Magadan

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Specific features of salmonid TRAV1 and TRAV22. (A). Multiple alignment of TRAV1 protein sequences from Atlantic salmon (Salsal) and rainbow trout (Oncmyk) with sequences presenting similar features from other Salmonids and other teleost. (B) IMGT Collier de Perles representation of Atlantic salmon TRAV1-1 based on the IMGT unique numbering for V-DOMAIN (45, 46). CDR1-IMGT is shown in dark blue and the CDR2-IMGT in light green and the germline CDR3-IMGT in dark green (33). Amino acids are shown in the one-letter abbreviation. Hatched circles correspond to missing positions according to the IMGT unique numbering (33, 46).(C) Salmon TRAV1 domain (cyan) aligned to human TR 2w20 alpha chain V domain. Position 23 is frame in red. (D) Multiple alignment of TRAV22 protein sequences from rainbow trout and Atlantic salmon with related sequences from other salmonids. (E) IMGT Collier de Perles of Atlantic salmon TRAV22-1. (F) Salmon TRAV22 domain (cyan) aligned to human TR lpha chain V domain. Note the long CDR3. The section of CDR3 encoded by TRAV22 is in red. 2nd-CYS104, additional Cys within the CDR3 loop, and Gly amino acids in di-Gly motifs (one in the G strand and one in within the CDR3) are highlighted. (C, G) Relative TRAJ usage shown as percentage of total reads containing a specific TRAJ gene among TRAV1-1, TRAV22, TRAV19-5 or TRAV19-9 containing productive rearrangements. Individual TRAJ genes are shown on the X-axis, average number of reads from each fish containing the indicated TRAV-TRAJ combination are shown (fish 1 is in green, fish 2 in orange and fish 5 in blue). The total number of sequences for each TRAV is indicated and the inlaid box shows the average representation of each TRAV per total number of productive rearrangements from each fish. (Atlantic salmon, Salmo salar: Salsal; rainbow trout, Oncorhynchus mykiss: Oncmyk; Brown trout, Salmo trutta: Saltru; Coho salmon, Oncorhynchus kisutch: Onckis; Chinook salmon, Oncorhynchus tshawytscha Onctsh; Chum salmon, Oncorhynchus keta: Oncket; Sockeye salmon, Oncorhynchus nerka: Oncner; Artic char, Salvelinus alpinus: Salalp; Lake trout, Salvelinus namaycush: Salnam; Three-spined stickleback, Gasterosteus aculeatus: Gasacu; Lumpfish, Cyclopterus lumpus: Cyclum; Olive flounder, Paralichthys olivaceus: Paroli; goby, Gobiodon reticulatus: Gobret, and Atlantic cod, Gadus morhua: Gadmor; guppy, Poecilia reticulata Poeret; sea bass, Dicentrarchus labrax: Diclab; barramundi perch, Lates calcarifer: Latcal).