Comparative genomics and transcriptomics of Steinernema carpocapsae and Caenorhabditis elegans

The evolution of the genome causes changes in gene expression which controls development and the regulation of these changes results in evolutionary modifications that consequently alter an organism’s function and adaptation. Studies of embryonic development in the sea urchin, Xenopus laevis, Caenorhabditis elegans, and other organisms have shown that developmental processes are a cascade of regulatory networks that determines developmental functions and these linkages have been conserved throughout evolution. While development has been extensively studied in the nematode C. elegans, less is known about the genomic architecture of development in other nematode species. We are interested in using C. elegans and distantly related entomopathogenic nematodes (EPNs), which are worms that parasitize and efficiently kill insects, from the genus Steinernema to study the similarities and differences in gene expression changes that give rise to similar body structures in these two species. First, we improved the genome and gene annotations of Steinernema carpocapsae to reliably conduct functional genomic analyses and to study responses to environmental changes via gene expression. Then, we compared two developmental stages, adults and infective juveniles (IJs), and the sexes of S. carpocapsae to equivalents in C. elegans. This comparison provided a set of conserved genes found in young adults and in another set in IJs. The comparison also gave insights into evolutionary changes to the regulation of gene expression which leads to similar morphological features. Subsequently, we profiled the transcriptomes of embryonic single cells from S. carpocapsae to identify founder cells that give rise to all the tissues in an adult worm. We used known C. elegans genes that determine the six founder cells, which give rise to all the body tissues, to identify these cells in S. carpocapsae and distinguish early embryonic cell fate. Lastly, to understand gene regulation we took a step towards C. elegans population genetics to emphasize within species variation in gene regulation. We compared the mRNA and microRNA profiles of twelve strains at the L1 stage. The comparison aimed to understand the differences in adaptation within one species to several differing environments. We found a set of 37 miRNAs that regulates gene expression at the L1 stage. Overall, all the approaches provide insights into the fundamental rules of gene expression that control changes at the genome and transcriptome level in development