Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

Abstract

BackgroundParasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri).ResultsWe used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis.ConclusionsWe have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein–DNA relationships shared between these two genera.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0746-6) contains supplementary material, which is available to authorized users.

Genomics of Entomopathogenic Nematodes and Implications for Pest Control

“…Manipulation of the bacterial partner is a strategy that may yield improvements in field efficacy related traits, but here we focus on the nematodes and the recently sequenced genomes [15, 16]. The availability of multiple EPN genomes should facilitate new and powerful studies of EPN biology and will be used to decipher the function of individual genes in parasitism [27, 28]. Here we discuss the implications that the recently available EPN genomes will have on their efficacy as biological control agents.…”

“…Artificial selection and hybridization can enhance desiccation tolerance [32–34], but removal of selection pressure ultimately results in loss of the desired traits [32, 33]. Deep knowledge of EPN genomes [27, 28], especially the genetic regulatory networks controlling the traits, coupled with improvements in genetic engineering for EPNs may provide new means to stabilize enhanced traits.…”

“…Analyses of these genomes revealed numerous genes that could be involved in parasitism by EPNs and are candidates for use in programs to improve traits for biological control [28]. Similar to what has been found in the H. bacteriophora genome, more than 10 000 predicted proteins (~37% of the predicted proteome) seem to have no orthologues in other animals or even other nematodes [28]. Studying the function of these orphan proteins could reveal genes important for infection or survival and persistence and thus be useful to future transgenic endeavours in EPNs.…”

Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq

“…We successfully utilized adapted versions of this protocol in the transcriptomic analysis of the insect-parasitic nematode, Steinernema carpocapsae (Lu et al ., 2017) as well as in the analysis of individual embryos and L1 larvae from two Steinernema and two Caenorhabditis species including C. elegans (Macchietto et al ., 2017), but this protocol can be adapted for any species of nematode. While this protocol will work on nematodes without already sequenced genomes or transcriptomes, we limit our computational analysis to organisms with published genome annotations, such as S. carpocapsae (Dillman et al ., 2015). Our need for single nematode RNA-sequencing arose as a method to circumvent the limitations of working with samples with low-inputs of RNA.…”

Introduction to Nematode Genome and Transcriptome Announcements in the Journal of Nematology

“…The famous laboratory model Caenorhabditis elegans was the first animal species to have its complete genome sequenced in the late 1990s (C. elegans Sequencing Consortium, 1998). This foundational achievement inspired many subsequent nematode genome sequencing efforts targeting more laboratory model species (Stein et al, 2003;Dieterich et al, 2008), animal-parasitic species (Ghedin et al, 2007;Hunt et al, 2016), entomopathogenic species (Bai et al, 2013;Dillman et al, 2015), and plant-parasitic species (Abad et al, 2008;Cotton et al, 2014). These efforts provided unprecedented scientific community resources leading to a diversity of new advances in biological disciplines ranging from ecology and evolution to human medicine to parasitology to nematology.…”