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. 2020 Jun 5;11(6):624. doi: 10.3390/genes11060624

Figure 3.

Figure 3

Evolutionary relationships of the eutherian mammalian TRGV genes. The TRGV as well as the TRGJ (Figure 4) and TRGC (Figure 5) gene sequences used for the phylogenetic analysis were retrieved from the IMGT® database (IMGT Repertoire, http://www.imgt.org) if annotated, or from the GenBank database using the accession numbers reported in the reference articles listed in Table 2 and Table 4. Chicken (Galgal) TRG genes were used as the outgroup [66]. For simplicity, we included in the analysis the TRGV genes belonging to a single species for each mammalian suborder in which the genomic organization of the TRG locus has been inferred. One member gene for each of the chicken (Galgal) TRGV subgroups was used as an outgroup. Multiple alignments of the V-region nucleotide sequences of functional genes and in-frame pseudogenes were carried out with the MUSCLE program [111]. The evolutionary analyses were conducted in MEGA7 [112]. We used the neighbor-joining (NJ) method to reconstruct the phylogenetic tree [113]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the branches [114]. The trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic trees. The evolutionary distances were computed using the p-distance method [115], and the units are the number of base differences per site. The analysis involved 66 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 176 positions in the final dataset. Monophyletic groupings described in the text are indicated by capital letters. The blue and red branches of the tree highlight two major groupings of the mammalian genes. The IMGT six-letter standardized abbreviations for species (Homsap (human), Musmus (mouse), Felcat (cat), Oviari (sheep), Camdro (dromedary), Turtru (dolphin), Orycun (rabbit)) and nine-letter abbreviations for subspecies (Canlupfam, dog) taxa are used.