Whole genome assembly and annotation of the clover root weevil (Sitona obsoletus) using a combination of Illumina, 10X Genomics and MinION sequencing

Abstract

AbstractWeevils are a highly diversified taxon, comprising about 70,000 described species that include many agricultural pests, biological control agents, and nutrient recyclers. Despite their importance and vast diversity, the number of sequenced genomes for the weevil family is still low (n=15). Here, we present a high-quality and contiguous genome assembly ofSitona obsoletus(Coleoptera: Curculionidae: Entiminae), a widespread invasive forage pest that infests clover species (Trifoliumspp.) worldwide. We sequenced, assembled, and annotated theS. obsoletusgenome using a hybrid approach that employed Nanopore long reads, 10X Chromium linked reads, Illumina short reads for assembly, and mRNA short read sequencing of various developmental stages for annotation. Our final annotated genome has a size of 1.2 Gb, with an N50 length of 313.85 kb. Benchmarking analyses against conserved single-copy Orthologs (BUSCO) found that over 94% of the genes were complete from each of the three BUSCO databases (Eukaryota, Insecta, and Arthropoda). A total of 9,777 protein-coding genes were annotated using the MAKER2 pipeline, of which 65% were functionally annotated. The annotated repeat elements make up 84.26% of the genome. The high-quality annotated genome of the weevil will facilitate a wide range of genetic, genomic, and phylogenetic studies on invasive weevils, as well as other weevil species in the subfamily Entiminae.