Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Page 3 of 19 Figure 1 Schematic representation of TRD gene exon-intron structures. (A) Representative structures of TRDV genes (based on genomic sequence for TRDV1au, GLEAN_15708), which contain two exons, and (B) the single TRDC gene (GLEAN_19705), which contains three exons, are shown. Scale is shown in base pair increments beneath the schematic. V-RS, recombination signal sequence of a V gene. Table 1 summarizes the proposed functional (or Open Reading Frame [ORF]) TRD genes that were identified within the bovine Btau_3.1 assembly. Most genes were identified within regions that were not placed on a chro- mosome (i.e. were found on ChrUn). However, it is expected that, like in primates and rodents, these genes are all located within the TRA/TRD locus which in cattle is on chromosome 10. The bovine consensus gene set (known as GLEAN) was used to identify gene prediction models of TRD genes. Where applicable, GLEAN num- bers are listed in Table 1, along with the Bovine Genome Scaffold identification number, location and orientation. It should be noted that the orientation of each contig individually, as well as in relation to other contigs, is not definitive at this point for the bovine Btau_3.1 assembly. All putatively functional (or ORF) genes (as determined based on criteria described in Methods) are shown. Based on analysis of flanking and intronic genomic sequence it was determined that many of these gene models might represent the same genes although they were found more than once. It is possible that this is due to an anomaly in the Btau_3.1 assembly, although it cannot be ruled out that those gene models do indeed represent duplicated genes that are present in the genome. 67 TRDV1, three TRDV2, two TRDV3 and one TRDV4 genes were identi- fied; after consideration of multiple gene models that might be representative of a single gene we propose the presence of 52 TRDV1, two TRDV2, one TRDV3 and one TRDV4 genes. The number of TRDV2, TRDV3 and TRDV4 genes is fairly consistent with what has been pre- viously reported [17,20], although evidence for two TRDV3 genes has been presented by others [20]. In addi- tion to the TRDV genes, five TRDD genes, three TRDJ genes and a single TRDC gene were identified, also con- sistent with previous reports [17,20]. The number of functional TRD genes among mamma- lian species is compared in Table 2. All species evalu- ated have genes for at least three TRDV subgroups. It is notable that humans have only a single TRDV1 gene (the mouse genes most closely related to human TRDV1 are named TRDV2-1 and TRDV2-2) while the TRDV1 subgroup in cattle and other artiodactyls are large, multigene families. Because of the disparity in numbers of TRDV1 genes in the human and cattle gen- omes, organization of their TRA/TRD loci cannot be compared. Furthermore, additional assembly of the bovine genome is required in order to definitively deter- mine the size of the TRA/TRD locus, to refine the gene organization, and to evaluate duplication events that resulted in the large TRDV1 subgroup. Schematic repre- sentations for regions in which three or more TRDV genes were identified are shown (Figure 2A). Schematics are shown to scale and gene orientation is as indicated, based on the Btau_3.1 assembly. As in other species, a single TRDC gene (see Figure 2B) as well as one TRDV gene located downstream of TRDC in an inverted tran- scriptional orientation (named TRDV4 in cattle) were identified [17]. In some cases multiple gene models