Figure 3.

Segmental duplications of Nlrp4 duplicates and V1r genes in the mouse genome. Figure 3a Comparison of gene relationships in the phylogenetic tree and their genomic position. Left: Phylogenetic tree of mouse Nlrp4 duplicates (including pseudogenes) and its closely related Nlrp5 and Nlrp9 genes. A total of 439 nucleotide sites are included in the final dataset. Right: Phylogenetic tree of 25 mouse V1r proteins whose encoding genes are located in the same genomic region as Nlrp4 genes. A total of 271 amino acid sites are included in the final dataset. The statistical confidence of each branch was estimated by the bootstrap method with 1000 replications, and only the values ≥ 80% are labeled in the trees. Middle: Genomic organization of related Nlrp and V1r genes. Five putative regions (I - V) might be concerned in segmental duplication. Figure 3b A possible scenario of segmental duplication deduced from synteny combining phylogeny: Genomic region I (involving Nlrp4b) and region II (involving Nlrp4d) might have been resulted from an early duplication, and the subsequence duplication events have given birth to region III (involving Nlrp4a) and region IV (involving Nlrp4c). Region V might have been duplicated later, and in this genomic region, other more recent segmental duplications (concerning pseudogenized Nlrp4 copy and V1rd genes) have been undertaken several times. We note that the order of duplication events in this potential scenario is mainly based on the topology of Nlrp4 phylogenetic tree. There might be other alternative itinerary to explain the present complex pattern of this genomic region.