Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Table 3 Features of bovine TRDV1 genes Phylogenetic Relationship to previously named set ovine sets [15]1 1NA indicates a bovine set lacking a related ovine set. Table 4 TRDV phylogenetic sets TRDV gene TRDV1 1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11 1C 1B 1D/1C 1A 1A 1A 1A 1E 1E 1E 1a, 1ac, 1af, 1b, 1h, 1k, 1l, 1m, 1n, 1s 1am, 1an 1az 1t 1aa, 1ah, 1ax, 1bm, 1bn, 1g, 1r 1c, 1aq 1aj, 1ap, 1ba, 1bd, 1d 1ag, 1aw, 1q 1bg 1bj 1bb 1bc, 1ao 1ad, 1p, 1x 1ae, 1ar, 1f 1o 1i, 1al, 1u, 1z 1w, 1j, 1bh, 1v, 1as 2-1, 2-2 3-1 4 [7.3.4] [7.3.4] [7.3.3] [8.3.4] [9.3.4] [9.3.4] [9.3.4] [9.3.4] [9.3.15] [9.3.12] [10.3.4] [5.3.4] [9.3.4] [7.0.4] [18.0.4] [7.3.4] [7.3.4] [7.3.5] [7.3.5] [7.5.4] TRDV2 TRDV3 TRDV4 1NA indicates TRDV subgroup for which no set is defined. 2For TRDV1 subgroup genes or subgroups (for the others). cDNA analysis as evidence for TRD gene usage Prior to these studies the number of TRDV1 genes found in the bovine genome, and their sequences, had not been resolved. Therefore, it was impossible to clas- sify cloned TRDV1 sequences based on their encoding genes. Furthermore, TRDV1 genes are highly poly- morphic but the subgroup also contains genes that differ by only one or three nucleotides in their coding regions (for example TRDV1aa and TRDV1bn, TRDV1v and TRDV1as). Therefore, it has been very difficult to differ- entiate between expressed TRDV1 sequences with regard to whether they represent the same or different genes. Here we classified previously-identified TRDV1 CDR1 length 7 7 9 9 9 9 5 or 10 9 7 7 7 G Y E Y Y Y or N A or V Y lacks CDR2 N or G G or V - +/- +/- - + - + + +/- + + CDR2 (amino acid at CDR3 (presence of W at Exceptions IMGT 57) IMGT 107) TRDV1 set1 Bovine genes in sets2 CDR-IMGT lengths Number of TRDV genes in each set2 Page 10 of 19 TRDV1t (CDR1 length of 8) TRDV1d (Q at IMGT-107) TRDV1o (CDR1 length of 18) 10 4 7 2 5 5 3 3 4 4 5 2 1 1 cloned cDNA sequences based on several criteria which included their relative placement in trees based on nucleotide and deduced amino acid sequences, specific sequence characteristics and percent identities based on nucleotide sequence alignments (data not shown). Results are summarized in Table 5 with the provisional IMGT nomenclature, corresponding genes and TRDV1 sets (as defined in Figure 4 and Tables 3 and 4) indicated. In some cases it was impossible to classify TRDV1 cDNA sequences definitively, because some TRDV1 genes share very high sequence identity; those cases are indicated in Table 5. Furthermore, in 20 cases (see