The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

Abstract

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.

Transcriptome Profile Changes Associated With Heat Shock Reaction in the Entomopathogenic Nematode, Steinernema carpocapsae

“…SOAP2 (version 2.2.1) 2 was used to filter out potential rRNA reads, and the data were filtered to be clean reads. The filtered clean reads were mapped to the reference genome, S. carpocapsae , using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) 3 ( Rougon-Cardoso et al, 2016 ). The assembled de novo transcriptome was implemented using Trinity ( Grabherr et al, 2011 ).…”

“…The transcriptomes and genomes of Steinernema spp. have been characterized (Dillman et al, 2015;Rougon-Cardoso et al, 2016;Yaari et al, 2016;Serra et al, 2019). However, no studies have focused on the specific genes and pathways involved in the heat shock reactions of S. carpocapsae.…”

Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae

“…In a previous study, nematodes in the Infective Juvenile (IJ) stage were induced with host insect ( Galleria mellonella ) tissues to detect differentially expressed proteins [12]. In that study, we conducted a qualitative analysis with which we identified 1,154 differentially expressed proteins.…”

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

“…The draft genome assembly of S. carpocapsae ALL strain had 1,578 contigs with an estimated genome size of 85.6 Mb, N50 of 300 kb and more than 28,000 predicted genes (Dillman et al , 2015). Another study, also using short-reads assembled S. carpocapsae Breton strain into 347 scaffolds with an N50 of 1.24 Mb (Rougon-Cardoso et al , 2016). The draft genome status, although helpful, can hinder further studies of protein families’ expansions involved in parasitism.…”