E3 ubiquitin-ligase-adaptor genes contribute to both gene family and genomic sequence divergence between C. nigoni and C. briggsae. (A–C) Bubble plot showing protein domain enrichment analysis for genes belonging to C. nigoni–specific dispensable gene families (as shown in Fig. 3B; A), genes located within interspecific unalignable regions of C. nigoni (as shown in Fig. 2A; B), and genes located within intraspecific divergent regions of C. nigoni wild isolates (as shown in Fig. 2B; C). The most significantly enriched domains, namely, F-box, BTB/POZ, and MATH, are highlighted. (D) Gene family expansion and contraction analysis across five Caenorhabditis nematodes. The predicted number of expanded (red) and contracted (green) gene families are indicated for each species as well as the ancestral node. (Cre) C. remanei; (Cbn) C. brenneri; (Cel) C. elegans. (E) Predicted numbers of expanded (red) and contracted (green) gene families encoding F-box, BTB/POZ, and MATH domain-containing proteins in each of the five nematode species as shown in panel D. (F–H) Chromosomal distribution of genes encoding proteins with F-box domains (F), BTB/POZ domains (G), and MATH domains (H) across all the C. nigoni strains. Relative chromosomal positions are used to account for differences in chromosome lengths across the strains.