Single-insect long-read sequencing enables the complete assembly of nuclear, mitochondrial and pathogen genomes in the coconut rhinoceros beetle, Oryctes rhinoceros

Here we present newly developed genomics resources for the fundamental and applied research of the coconut rhinoceros beetle, Oryctes rhinoceros. Populations of this invasive agricultural pest have been suppressed for decades, but their expansions across the Pacific islands since 2007 suggest that one of the key tools in the control arsenal, Oryctes nudivirus, might be losing its efficacy. Using long read nanopore sequencing of DNA extracted from a single wild-caught O. rhinoceros female and supplemental Illumina short read sequences, we created the complete circular assemblies for the mitochondrial O. rhinoceros genome, and genome of the biocontrol agent Oryctes nudivirus. For the nuclear genome assembly, we achieved one of the highest levels of contiguity (N50: 9.77 Mb; L90: 47) and completeness (n:2124 BUSCOs, C:97.9%, M:0.9%) among available coleopteran genome assemblies. The complete mitogenome sequence will enable further development of molecular markers that could be used for high-throughput diagnostics of incursive samples in biosecurity and integrated pest management programs. The long-read sequencing also enabled the discovery of structural variants in the nudivirus isolate, (inverted gene group, insertion/deletion of amino acids, loss of coding sequences etc.), that will facilitate further investigation into the putative effects of these changes that could lead to the suspected reduced virulence of this biocontrol agent. Our genomics resources are expected to facilitate research into the biology and dynamics of invasive populations of O. rhinoceros, as well as comparative analyses for related agricultural pests.