The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822)

We present a genome assembly from an individual female Eupeodes luniger (the Common Spotted Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 616.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.


Background
The Common Spotted Hoverfly, Eupeodes luniger, is a mediumsized yellow and black hoverfly that is thought to be a Batesian mimic of social wasps to protect itself from predators (Golding et al., 2005).Both males and females have yellow lunate comma shaped markings on their black abdomens (Ball & Morris, 2015).In the UK this is the most common Eupeodes, yet males especially can be difficult to separate from other Eupeodes species (Stubbs & Falk, 2002).The females, however, are readily identifiable and have a dark Y-shaped mark in front of the ocelli (Stubbs & Falk, 2002).
Adult E. luniger hoverflies utilise the protein from pollen for egg maturation, making them important pollinators (Doyle et al., 2020;Rotheray, 1993).The larvae of these flies are aphidophagous on a wide range of aphid species in a variety of habitats (Jamali et al., 2018;Rotheray, 1993).Therefore, they play an important ecological role in the form of pest control.This makes them a potentially useful species for integrated pest management (IPM) approaches.E. luniger is a migrant hoverfly, as is the similar Eupeodes corollae (Sivell et al., 2023), but may have a more resident population as peaks in abundance are seen earlier in the spring as well as in the summer (Ball & Morris, 2015;Hlaváček et al., 2022).This is the first whole genome sequence for Eupeodes luniger, and we believe that the sequence described here, generated as part of the Darwin Tree of Life project, will further aid understanding of the biology and ecology of this hoverfly.

Genome sequence report
The genome was sequenced from one female Eupeodes luniger (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 40-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 177 missing joins or mis-joins and removed 15 haplotypic duplications, reducing the assembly length by 0.9% and the scaffold number by 58.04%, and increasing the scaffold N50 by 120.28%. The final assembly has a total length of 616.9 Mb in 59 sequence scaffolds with a scaffold N50 of 320.0 Mb (Table 1).A summary of the assembly statistics is shown in Figure 2, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.79%) of the assembly sequence was assigned to 4 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).We did not identify the X chromosome as sequence data from the heterogametic sex was not available and homology is unreliable for sex chromosome identification in Diptera due to frequent sex chromosome turnover (Vicoso & Bachtrog, 2015).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/1124559.

Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing was a female Eupeodes luniger (specimen ID Ox000159, ToLID idEupLuni2).A second female Eupeodes luniger (specimen ID Ox000147, ToLID idEupLuni1) was used for RNA sequencing.Both specimens were netted in Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2019-08-07.The specimens were collected and identified by Will Hawkes (University of Exeter) and snap-frozen on dry ice.The idEupLuni2 sample was prepared for DNA extraction at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The specimen was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Head and thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.RNA was extracted from abdomen tissue of idEupLuni1 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format  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: (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 "sangertol/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.Table 3. Software tools: versions and sources.

Software tool Version
Major comments: none Minor comments: none While the particular organism and its genome sequence are interesting in their own right, the continued generation of high quality genomes by the Darwin Tree of Life project team will underpin a great deal of future work on evolutionary biology.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Computational biology, genomics, transcriptomics, parasitology, developmental biology I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Is the rationale for creating the dataset(s) clearly described? Yes
Are has not yet been vetted by external experts in the field.This is a critical step in the scientific process that will ultimately strengthen the credibility of the findings.
2. **Potential for Further Analysis:** The genome assembly lays the groundwork for in-depth functional annotation, which could reveal key genes and their roles in the hoverfly's biology.Future research could focus on annotating the genome to enhance our understanding of the species' unique characteristics and evolutionary adaptations.
3. **Comparative Genomics:** The genome sequence offers a valuable resource for comparative genomics studies with related species.Such comparisons could shed light on the genetic underpinnings of the hoverfly's distinctive traits and its adaptive evolutionary history.This represents an area ripe for further exploration.
I believe the article on the Common Spotted Hoverfly's genome sequence provides an invaluable resource for future research endeavors and has the potential to inform agricultural practices and conservation strategies.
Is the rationale for creating the dataset(s) clearly described?Yes Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Eupeodes luniger, idEupLuni2.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 616,908,419 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (319,955,300 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (319,955,300 and 131,323,115 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the diptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idEupLuni2.1/dataset/CATOCI01/snail.

Figure 5 .
Figure 5. Genome assembly of Eupeodes luniger, idEupLuni2.1:Hi-C contact map of the idEupLuni2.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=OEGHJP_7S0uMmC-mntHIrA.

Table 2 . Chromosomal pseudomolecules in the genome assembly of Eupeodes luniger, idEupLuni2. INSDC accession Chromosome Length (Mb) GC%
Table3contains a list of relevant software tool versions and sources.Wellcome Sanger Institute -Legal and GovernanceThe materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the '

Darwin Tree of Life Project Sampling Code of Practice', which
can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.

the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Partly Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.myreview of the manuscript and I am pleased to report that I found no significant issues requiring further attention.The article is well-crafted, with a clear and concise presentation of the research topic, robust methodology, and sound analysis.The results are wellsupported and the discussion is insightful, providing valuable contributions to the field.**MajorPoints:** 1. **Scientific Significance:** The publication is a notable achievement as it presents the inaugural genome sequence for Eupeodes luniger, enriching our understanding of this species' biology and ecology.The genome sequence opens doors to investigate evolutionary patterns, genetic diversity, and the functional aspects of the hoverfly's genetics.2.**Genome Assembly Quality:** The quality of the genome assembly is commendable, with a substantial contiguity.The meticulous use of Hi-C data for scaffolding, along with manual curation, demonstrates a high level of precision and attention to detail in the assembly process.Peer Review Status:** The article, at the time of its initial publication, was awaiting peer review.This indicates that while the research is presented by respected institutions, it © 2024 Guan D.