Comparative Genomics of Steinernema reveals Deeply Conserved Regulatory Networks in Nematodes Steinernema sp.

Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as entomopathogens, deadly parasites of insects used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four sister species (S. scapterisci, S. monticolum, S. feltiae, S. glaseri), which are distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes in Steinernema and C. elegans. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs that are associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution.