Reduced signatures of gene duplication and non-random gene organization in shaping stage-specific patterns of gene expression across a relatively simple life cycle

Complex eukaryotes generally experience some degree of ecological transition as they develop, which is usually accompanied by the expression of different traits across their ontogeny. Theory suggests the evolution of differentiation between life stages is facilitated by the expression of different genes at different points throughout ontogeny, which alleviates pleiotropic 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 on chromosomes have been identified as important features of relatively complex ontogenies. Therefore, one could predict that their link to transcriptional specialization across ontogeny may be weaker in relatively simpler life cycles. 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, our findings add to a body of evidence that suggests a link between gene duplication and gene organization and the evolution of complex ontogenies.