The genome sequence of the small spotty-eyed dronefly, Eristalinus sepulchralis (Linnaeus, 1758) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual female Eristalinus sepulchralis (the small spotty-eyed dronefly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 376.8 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.96 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,752 protein coding genes.


Background
The small spotty-eyed dronefly, Eristalinus sepulchralis (Linnaeus, 1758), is a European hoverfly species which is widespread in the UK and is most commonly found in the southern lowlands in highest abundance between June and August, though they can be encountered from any time from April to October (Ball & Morris, 2000;Ball & Morris, 2015). Concerningly, records of this hoverfly indicate numbers have significantly diminished during recent years (Ball & Morris, 2015).
Eristalinus sepulchralis give rise to rat-tailed aquatic larvae which are most frequently observed in habitats closely associated with farmland drainage, including decaying organic matter in ponds and wet manure (Rotheray, 1993). As adults, E. sepulchralis remain close to these agricultural areas and can regularly be found interacting with a wide variety of local floral resources and basking in sunny spots (van Veen, 2010); they also overwinter as adults in sheltered locations (Ball & Morris, 2000). Small spotty-eyed droneflies are stocky, metallic looking hoverflies, their most recognisable feature being their beige coloured eyes speckled with characteristic dark brown spots that are entirely covered in hairs, a detail which sets them apart from the closely related Eristalinus aeneus, the other UK Eristalinus species, which lack hairs on the lower half of the eyes (Ball & Morris, 2015). The completed genome sequence for Eristalinus sepulchralis is an important resource in aiding the study of this hoverfly species, potentially contributing to the identification of any genetic components involved in its recent decline.

Genome sequence report
The genome was sequenced from one female Eristalinus sepulchralis ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.33). A total of 44-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 304 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 71.16%, and decreasing the scaffold N50 by 46.35%.
The final assembly has a total length of 376.8 Mb in 76 sequence scaffolds with a scaffold N50 of 66.5 Mb (Table 1). Most (99.17%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds, representing 5 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/2725509.

Sample acquisition and nucleic acid extraction
The specimen selected for genome sequencing was a female Eristalinus sepulchralis (specimen ID Ox000764, idEriSepu1) was netted in Wytham Woods, Oxfordshire (biological vicecounty Berkshire), UK (latitude 51.77, longitude -1.33) on 2020-08-04 by nett. The specimen was collected and identified by Steven Falk (independent researcher) and then snap-frozen on dry ice.
The specimen used for RNA sequencing (specimen ID NHMUK014036950, idEriSepu2) was collected in Cothill Fen National Nature Reserve, UK (latitude 51.69, longitude -1.32) by Olga Sivell, Duncan Sivell and Ryan Mitchell   sequencing were performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from head tissue of idEriSepu1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023). The assembly was checked for contamination and corrected as described previously (Howe et al., 2021). Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022). The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2022), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020). This work was done using Nextflow (Di Tommaso et al., 2017) DSL2 pipelines "sanger-tol/readmapping" (Surana et al., 2023a) and "sanger-tol/genomenote" (Surana et al., 2023b). The genome was analysed within the BlobToolKit environment (Challis et al., 2020) and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.  Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021)  The genome sequence is released openly for reuse. The Eristalinus sepulchralis genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.