Murad, Rabi et al. (2015) International Worm Meeting "A modular framework for teaching sequencing based functional genomics to high school students.."

Macchietto, Marissa, Murad, Rabi, Mauzy-Melitz, Debra, Mortazavi, Ali

[International Worm Meeting, 2015]

Living organisms rely on genes to manage all aspects of their lives. Although all of the cells in an organism possess the exact same genetic code, they can specialize to form different tissues and organs by selectively expressing particular sets of genes at particular times. We designed a modular course to introduce high school students to these major genetic concepts and the sequencing technologies that are now revolutionizing the field of genomics. The course focuses on nematodes of the genus Steinernema, insect parasites with broad scientific and commercial applications. Each module achieves specific teaching goals, and they can be used alone or in combination to meet the particular needs of individual instructors. Using this approach, we were able to guide students through all the stages of a modern genomics experiment: culturing the organism of study, isolating RNA from different stage of Steinernema life cycle, sequencing the libraries, and then analyzing the data using open-source computational tools. Students reacted positively to their hands-on experience performing the RNA-seq assay and analyzing the data they generated, but they especially enjoyed being given the opportunity to design their own projects based on the nematodes. Overall, we have demonstrated that sequencing assays and genomics can be taught to high school students, and that this course format makes this field more accessible to teachers and students at the secondary and post-secondary levels.

Serra, Lorrayne et al. (2019) International Worm Meeting "Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome."

Macchietto, Marissa, Murad, Rabi, Maya Rodriguez, Isaryhia, Serra, Lorrayne, Macias-Munoz, Aide, Mortazavi, Ali, Rodriguez, Bryan, Joan McGill, Cassandra

[International Worm Meeting, 2019]

Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome of S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae's chromosome X to be primarily orthologous to C. elegans' and P. pacificus' chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.