Mechanisms of IR repertoire expansion.
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(A) Genomic location of the IR genes (black arrowheads; pseudogenes in grey) belonging to the IR94 and IR52 clades in D. melanogaster, D. sechellia, D. ananassae and D. virilis. Equivalent chromosome arms (Muller elements) (labelled on the left of each chromosome arm) between the species are indicated by colour and horizontal alignment . Tandem arrays of genes are indicated by horizontal black lines, and the distances between close arrays are shown. The “IR” and some number prefixes for gene names are omitted in clusters where space is limiting. The scale bar represents 20 Mb for the chromosomes and 30 kb for gene lengths and distances between genes within the same tandem array. (B) Phylogenetic tree of D. melanogaster iGluRs and IRs, in which branches are colour-coded by the number of introns in each extant gene sequence or predicted ancestor. The tree was built with RAxML under the WAG model of substitution, with 1000 bootstrap replicates, and the colours representing intron numbers were inferred and displayed with Mesquite. Pseudogenes were excluded from this analysis. The scale bar represents the expected number of substitutions per site. (C) Histogram illustrating the distribution of intron positions as a percentage of protein length for iGluRs and antennal IRs (blue) and divergent IRs (red). Each bar represents the probability of occurrence of an intron at a given percentile of the protein.