Fig. 1

IR conservation in mammalian and vertebrate species. a Phylogenetic tree of species under investigation and morphology of FACS sorted human, mouse, dog, chicken, and zebrafish granulocytes (Mya = million years ago) following Giemsa or Wright staining. The horizontal bar plot shows the fraction of expressed genes affected by IR in each species. b The five-way symmetric Venn diagram shows the intersections of orthologous intron-retaining genes between species. Eighty-six orthologs are conjointly affected by IR in all five species. The three-way asymmetric Venn diagram shows the intersecting gene sets of intron-retaining orthologs in placental mammals (human, mouse, dog), while the asymmetric two-way Venn diagram below illustrates the intersection of intron-retaining orthologs in the non-placental vertebrates (chicken and zebrafish). c Circos plot illustrating links between genes and annotation terms that are repeatedly enriched in the species-specific gene clusters. The right semicircle depicts the enriched terms. The left semicircle includes five concentric rings that represent color-coded IR ratios of orthologous genes in all five species, starting from human (H), mouse (M), dog (D), chicken (C), and zebrafish (Z). Left: A magnified section of the concentric rings. Orthologous genes sometimes do not have consistent IR values across the species; however, the IR functional specificity is conserved by targeting functionally related genes. A scalable version of this figure in vector format is provided in Additional file 5. d IR data from granulocytes exhibits a strong anti-correlation (Pearson correlation; r = –0.95) between the fraction of expressed intron-retaining genes and the number of protein-coding genes in a genome. e Number of retained introns per kbp exon sequence in relation to the average number of introns per kpb exon sequence in a genome