Validation of reference-assisted assembly using existing and novel Heliothine genomes

Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran family with few genomic resources. We then examined the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa and applied it to our Heliothine genomes. Our work demonstrates that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. We conclude by discussing both the potential and pitfalls of reference-assisted assembly according to the intended downstream assembly application.