Whole genome assembly and annotation of the lucerne weevil Sitona discoideus

Abstract

Weevils are a diverse insect group that includes many economically important invasive pest species. Despite their importance and diversity, only nine weevil genomes have been sequenced, representing a tiny fraction of this heterogeneous taxon. The genus Sitona consists of over 100 species, including Sitona discoideus (Coleoptera: Curculionidae: Entiminae), commonly known as lucerne (or alfalfa root) weevil. Sitona discoideus is an important pest of forage crops, particularly Medicago species. Using a dual sequencing approach with Oxford Nanopore MinION long-reads and 10x Genomics linked-read sequencing, we generated a high-quality hybrid genome assembly of S. discoideus. Benchmarks derived from evolutionarily informed expectations of gene content for near-universal single-copy orthologs comparison (BUSCO) scores are above 96% for single-copy orthologs derived from eukaryotes, arthropods, and insects. With a de novo repeat library, Repeatmasker annotated 81.45% of the genome as various repeat elements, of which 22.1% were unclassified. Using the MAKER2 pipeline, we annotated 10,008 protein-coding genes and 13,611 mRNAs. Furthermore, 68.84% of total predicted mRNAs and 67.90% of predicted proteins were functionally annotated to one or more of InterPro, gene ontology, and Pfam databases. This high-quality genome assembly and annotation will enable the development of critical novel genetic pest control technologies and act as an essential reference genome for broader population genetics and weevil comparative genetic studies.