The growing nutritional demand of the world population poses great challenges to sustainable and productive agriculture. Entomopathogenic nematodes (EPNs) are an economically interesting alternative to traditional methods of pest control, despite poorly understood aspects of their biology and genomics. This study provides a comprehensive characterization of the genome of Heterorhabditis bacteriophora and its capacity to resist benzoxazinoids that are sequestered as defense compounds by an important insect pest. We performed a de novo chromosome-scale assembly of the H. bacteriophora genome and compared it with the genomes of other nematodes, highlighting syntenic orthologs and genome organization in EPNs. Co-phylogenetic analyses and genetic structure data of several H. bacteriophora isolates and their Photorhabdus symbionts suggest divergent evolutionary scenarios of these two species groups. Population genomics analyses within H. bacteriophora identified genetic variation distinguishing between strains susceptible and resistant to benzoxazinoids. Genome-wide differentiation (FST) pointed to genomic regions related to deoxyribonucleotide biosynthetic processes, polypeptide N-acetylgalactosaminyltransferase activity and single-stranded DNA endodeoxyribonuclease activity that were shaped by strong selective pressures. Having identified candidate genes associated with insect pathogenicity and benzoxazinoid resistance, our findings provide a foundation for future work on the efficacy and infectivity of EPNs in pest management.

Bryophytes’ remarkable capacity to tolerate extreme abiotic conditions allows us to enhance our understanding of the diversity of molecular mechanisms involved in plant stress response. Here, we used next generation sequencing to study DNA methylation and gene expression changes in plants from four populations of the metallophyte moss Scopelophila cataractae experimentally exposed to either Cd or Cu. These populations previously showed differences in tolerance to both metals, so here, we aimed at uncovering the molecular basis of this phenotypic differentiation. We found no evidence of genetic differentiation among the populations studied. The epigenetic data, however, showed limited but significant population-specific changes in DNA methylation in response to both metals. Exposure to acute Cu stress in the laboratory led to the downregulation of genes involved in heavy metal tolerance in both populations regardless of their tolerance level, but this response was quantitatively higher in the most tolerant. We propose that chronic exposure to varying levels of heavy metals in the field led to potentially non-genetically-based intraspecific differentiation for heavy metal tolerance in S. cataractae. The most tolerant plants invested more in constitutive protection and were more efficient in entering a conservative state when faced with acute Cu stress.