Comparative genomics of Steinernema

Nematodes comprise one of the most diverse bilaterian phyla, having colonized nearly every imaginable ecological niche on earth. They are major parasites of plants, animals, and humans, despite sharing a relatively conserved body plan. The Steinernema genus comprises over 70 characterized species that are lethal parasites of insects, which have different foraging strategies and host ranges, and are distantly related to the model organism C. elegans. To better understand the evolution of parasitism and development in nematodes, we sequenced and analyzed the genomes as well as transcriptomes of five key members of the Steinernema genus (S. carpocapsae, S. scapterisci, S. monticolum, S. glaseri, and S. feltiae). In chapter 2, using available ecological and molecular data, we explore genomic differences likely to be involved in insect parasitism, particularly in host-range and specificity of these five species. We find surprising gene family evolution of proteases, protease inhibitors, proteolytic cascade proteins, GPCRs, transposon and retroviral content, and even protein-protein interaction domains, many of which correlate excitingly with known differences in host range and specificity among these parasites. The combination of multiple closely related genomes in a non-Caenorhabidtis clade and accompanying deeply sequenced transcriptomes allows for powerful comparisons to other genera such as Caenorhabditis. In particular, comparisons in gene expression at defined stages show surprising plasticity of timing across one-to-one orthologous genes in the five genomes when compared to C. elegans. Our conservation analysis shows that approximately 20 Mb are conserved across the Steinernema species, with 5.1 Mb of this comprising non-coding regions. Our analysis of the conserved non-coding regions combined with stage-specific gene expression data reveals that a limited number of regulatory motifs are associated with conservation of stage-specific ortholog expression in Steinernema and Caenorhabditis, which suggests that several underlying gene regulatory relationships controlling development are conserved in the two genera. In Chapter 3, we investigate embryonic development in Steinernema by comparing the expression of orthologous genes at eleven different embryonic stages of two Steinernema species with two Caenorhabditis species. We found that zygotic transcription initiates at different developmental stages in each species, with the Steinernema species initiating transcription at earlier developmental stages than Caenorhabditis. Surprisingly, we also found that gene expression conservation during development is highest at the later embryonic stages than at the earlier ones, indicating that ortholog expression divergence across distantly related species follows a funnel-shaped model in contrast to the hourglass model of nematode development that has been previously proposed. Thus, this work provides novel insight into embryonic development across distantly related nematode species and demonstrates that the mechanisms controlling early development are more diverse than previously thought