Reduced signatures of gene organization and duplication in shaping stage-specific patterns of expression across the <i>C. elegans</i> life cycle

Complex eukaryotes generally express different traits as they grow and develop to facilitate their function in different ecological niches. Theory suggests the evolution of differentiation between life stages is facilitated by the expression of different genes at different points throughout ontogeny, which alleviates evolutionary constraints. Therefore, ascertaining what contributes to specialized patterns of gene expression across ontogeny is fundamental to understanding the evolution of ontogenetic complexity. Expression divergence between duplicate genes and gene organization have been identified as important features of relatively complex ontogenies. Therefore, one could predict that their link to transcriptional specialization may be weaker across relatively simpler ontogenies. Here, we investigated the links between gene duplication, gene organization, and stage-specific patterns of expression across the relatively simple Caenorhabditis elegans life cycle. We found that signatures of stage-biased chromosomal regions were weaker in C. elegans than what has been previously described in organisms with more complex ontogenies. Furthermore, we found the extent that duplicate genes varied in ontogenetic expression pattern was more constrained in C. elegans. Overall, these findings help generalize our understanding of the association between gene duplication, gene organization, and the evolution of complex ontogenies.