High-quality genome assemblies for nine non-model North American insect species representing six orders (Insecta: Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera).

ABSTRACT

Field-collected specimens were used to obtain nine high-quality genome assemblies from a total of 10 insect species native to prairies and savannas of central Illinois (USA) Mellilla xanthometata (Lepidoptera Geometridae), Stenolophus ochropezus (Coleoptera Carabidae), Forcipata loca (Hemiptera Cicadellidae), Coelinius sp. (Hymenoptera Braconidae), Thaumatomyia glabra (Diptera Chloropidae), Brachynemurus abdominalus (Neuroptera Myrmeleontidae), Catonia carolina (Hemiptera Achilidae), Oncometopia orbona (Hemiptera Cicadellidae), Flexamia atlantica (Hemiptera Cicadellidae) and Stictocephala bisonia (Hemiptera Membracidae). Sequencing library preparation from single specimens was successful despite extremely small DNA yields (<0.1 µg) for some samples. Additional sequencing and assembly workflows were adapted to each sample depending on the initial DNA yield. PacBio circular consensus (CCS/HiFi) or continuous long reads (CLR) libraries were used to sequence DNA fragments up to 50 kb in length, with Illumina sequenced linked-reads (TellSeq libraries) and Omni-C libraries used for scaffolding and gap-filling. Assembled genome sizes ranged from 135 MB to 3.2 GB. The number of assembled scaffolds ranged from 47 to >13,000, with the longest scaffold per assembly ranging from ~23 to 439 Mb. Genome completeness was high, with BUSCO scores ranging from 85.5% completeness for the largest genome (Stictocephala bisonia) to 98.8% completeness for the smallest genome (Coelinius sp.). The unique content was estimated using RepeatMasker and GenomeScope2, which ranged from 50.7% to 75.8% and roughly decreased with increasing genome size. Structural annotation predicted a range of 19,281-72,469 protein models for sequenced species. Sequencing costs per genome at the time ranged from US$3-5k, averaged ~1600 CPU-hours on a high-performance cluster and required approximately 14 h of bioinformatics analyses with samples using PacBio HiFi data. Most assemblies would benefit from further manual curation to correct possible scaffold misjoins and translocations suggested by off-diagonal or depleted signals in Omni-C contact maps.