FIG. 1.

Conserved synteny and phylogenetic clustering indicate that feTRIM5 is a true TRIM5 orthologue. (A) Paralogues TRIM6, TRIM34, TRIM5, and TRIM22 are found in a cluster in the human and dog genomes and in the 1.9-fold cat genome project. In all of these cases, the cluster is surrounded by olfactory genes. Exons 2 (ex2) and 8 (ex8) of the pseudogenized dog TRIM5 sequence are shown. Other genes in cat as well as dog TRIM6 are predicted genes or regions of homology only and may not be expressed or functional. ch, chromosome. (B) Neighbor-joining tree of TRIM5 orthologues from several mammalian species. feTRIM5 clusters with other TRIM5 orthologues in preference to closely related paralogues TRIM34, TRIM6, and TRIM22 and the more distantly related paralogue TRIM21. Moreover, the TRIM5 phylogeny reflects established mammalian evolutionary relationships. Numbers indicate bootstrap values after 1,000 iterations, and branch length reflects the number of base substitutions per site. Nucleic acid sequences were codon optimized and aligned by using ClustalW with manual adjustment. All of the positions containing gaps were eliminated from the data set.