Abstract
Invasive species can cause significant environmental and economic damage. Weevils are an economically important insect group comprising 70,000 described species, many of which are invasive. Despite their enormous diversity and significance, genetic resources for invasive weevils are scarce compared with insects of other taxa. Among the invasive weevils, Sitona obsoletus (clover root weevil), S. discoideus (lucerne weevil), and Listronotus bonariensis (Argentine stem weevil) are significant agricultural pests in many parts of the world, including New Zealand. The collective impact of these weevils is estimated to result in a yearly loss of 600 million dollars to New Zealand’s pastoral agriculture sector, posing a significant challenge to the current control strategies.
This study presents the annotated whole genome assemblies of S. obsoletus and S. discoideus, representing the first genomes sequenced for this widespread genus that comprises over 100 species. The genome of L. bonariensis has been sequenced. Sequencing the genome of an organism is the first step to understanding different aspects of its biology, evolution, and genetic complexities and interactions with environment. I used a hybrid approach combining Nanopore long-read, 10X Genomics linked-read, and Illumina short-read technologies to sequence and assemble the S. obsoletus and S. discoideus genomes. The final annotated genomes of S. obsoletus and S. discoideus were 1.2 Gb and 0.94 Gb in size respectively. Benchmarking analyses against conserved single copy orthologs (BUSCO) showed that over 94% of the genes were complete in both genomes across the three BUSCO databases (Eukaryota, Insecta, and Arthropoda). In addition, 9,777 and 10,008 protein-coding genes were annotated using the MAKER2 pipeline for S. obsoletus and S. discoideus genomes, respectively. Annotated repeat elements comprised 84.26% and 81. 45% of the genome, which is higher than any weevil genome sequenced to date. The high-quality annotated genome assemblies of Sitona species will serve as a valuable genomic resource for functional genetic research for developing novel pest control tools and conducting broader population genetics and comparative genomics studies.
In addition to the genomes, I also examined the microbial composition, diversity, and richness of three invasive weevil species (S. obsoletus, S. discoideus, and L. bonariensis) using the 16S rRNA Amplicon Sequencing approach. Microbial communities in insects play crucial roles in the biology, ecology, and evolution of their hosts. This study identified 1,112 bacterial operational taxonomic units belonging to 17 phyla, with Proteobacteria and Actinobacteria being the most dominant. The study observed distinct microbial compositions and diversity between the weevil species and their collection sites. This study identified Rickettsia as a potential key player in the S. obsoletus microbiomes and Buchnera in L bonarensis. Moreover, Buchnera abundance was observed to be significantly reduced in parasitised L. bonarensis compared to unparasitised samples, which might have implications for the declining effectiveness of parasitism success by its parasitoid, Microctonus hyperodae. With further study, these microbiomes can potentially be exploited to develop novel pest control tools. The resources and information gathered in this study will be useful for further investigating the functions of microbes in weevil biology, immunity, and interactions with their parasitoids through microbiome manipulation studies.