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Abstract

The development and metabolism of nematodes can be significantly impacted by the microbes in their environment. Adaptation to environmental stimuli may also be facilitated by the creation of new genes. About one third of genes in the nematode Pristionchus pacificus are characterized as taxonomically-restricted orphan genes, i.e. genes whose function can't be inferred from homology. Our main goal is to gain insight on the interactions between P. pacificus and bacterial food sources by answering two questions: do novel genes contribute to environmental adaptation and which are the bacterial metabolites that modulate the environmentally responsive networks containing those novel genes. To that end, we generated transcriptomes of P. pacificus adult worms on different bacterial strains isolated from Pristionchus associated environments and used coexpression to uncover the regulatory networks responding to microbiota. This approach also identified orphan genes that have integrated into environmentally responsive networks. To explore how metabolic pathways in the worm are regulated by the presence/absence of bacterial metabolites, we generated bacterial genome assemblies and computationally identified the bacterial metabolic pathways present. This allowed us to correlate the metabolic potential of bacteria with various nematode traits including survival, chemoattraction and the response of the identified co-expression modules.