Chromosome-scale genome assembly and annotation of the goldenrod gall fly, Eurosta solidaginis (Fitch) (Diptera: Tephritidae).

Eurosta solidaginis is a plant-parasitic insect that develops from egg to adult inside of a spheroid gall it induces on the stem of goldenrod plants (Solidago spp.). E. solidaginis is widespread across North America, with a geographic distribution that extends from Southern Canada to Texas and the Southern U.S. and from the Atlantic coast to the Great Plains and includes scattered populations reaching the West coast. The natural history, ecology and physiology of E. solidaginis are well-documented, and its overwintering physiology, multitrophic interactions, and ecological speciation have been well-studied. Surprisingly, genomic resources are restricted to an incomplete scaffold-level genome assembly lacking protein-coding gene annotation. To advance understanding of the physiology, gall-forming, and population structure of E. solidaginis, we sequenced and assembled the genome of a single pupa using PacBio HiFi sequencing and Hi-C chromatin proximity sequencing technology. Here, we present a fully-annotated, chromosome-level de novo assembly of the 1.9 Gb genome, spanning five autosomes and the sex chromosomes. The assembly has a contig N50 of 3.7 Mb and a scaffold N50 of 289.3 Mb, and 96.5% of expected Diptera BUSCOs in the genome found in single copy. We annotated 14,223 identified protein-coding genes, identifying 96.2% of BUSCOs in the protein set found in single copy. The 18,293 bp mitochondrial genome was assembled and subsequently annotated separately. Even though there are 400-450 gall-inducing tephritid species, this is the second high-quality, chromosome-level genome assembly of a gall-forming fly in the family, and the third freeze tolerant dipteran genome.