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Fig. 4 | Genome Biology

Fig. 4

From: Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Fig. 4

Distribution of transcription factor (TF) families across insect genomes. a Heatmap depicting the abundance of 74 TF families across 16 insect genomes (Hemiptera highlighted in red text), with Daphnia as an outgroup, based on the presence of predicted DNA binding domains (see the “Methods” section). The color key has a log (base 2) scale (light blue means the TF family is completely absent). Values are in Additional file 2: Table S6.3. b Bar graph showing the number of proteins of each of the 2 most abundant TF families, homeodomains and C2H2 zinc fingers (ZFs), per species using 4-letter abbreviations (full names in a). Solid lines demarcate insect orders: Hemiptera (Hemipt.), Hymenoptera (Hym.), Coleoptera (Col.), and Diptera (Dipt.). The dashed line demarcates the dipteran family Culicidae (mosquitoes). c Proportions of Oncopeltus homeodomain (HD) and C2H2 zinc finger proteins with orthology assignment (predicted DNA binding specificity) and/or manual curation. “Classified” refers to the automated classification of a protein to a TF family, but without a specific orthology assignment. d Maximum likelihood phylogeny of representative subsets of the zinc finger 271-like family in Oncopeltus (49 proteins, blue text) and the pea aphid (55 proteins, black text), with chelicerate (red text) and holometabolan (yellow text) outgroups (16 proteins, 7 species), based on the Oncopeltus OGS and GenBank protein accessions. Gaps were removed during sequence alignment curation; all nodes have ≥ 50% support; branch length unit is substitutions per site [157]. Key nodes are circled for the clades containing all aphid or all Oncopeltus proteins (82% support each), and each “core” clade comprised exclusively of proteins from each species (97% and 100%, respectively; triangles shown to scale for branch length and number of clade members). Branch length unit is substitutions per site. Analyses are based on OGS v1.1

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