The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840)

We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 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 16.87 kilobases in length.


Background
Cheilosia impressa is a broad-bodied, medium-sized hoverfly (wing length 5.75-8 mm), with a European and eastern Palaearctic distribution (Speight, 2017).As with many Syrphidae, males and females are easily teased apart by compound eye dimorphism, however the females of C. impressa also possess distinctive yellow wing bases and males have red eye colouration (Ball & Morris, 2013).Cheilosia species can be distinguished from similar species by the presence of a zygoma -a defined margin between the eye and the face unique to the Cheilosiini tribe.C. impressa is strongly associated with woodland edges, rides, and roadside verges when umbellifers are in bloom between May and August (Speight, 2017).The UK distribution of this species is mainly southern, although there is some occurrence in regions as north as Scotland (Ball & Morris, 2013).
Investigation of hoverfly evolutionary ecology, using mitochondrial genomes of 127 species has recently revealed rapid diversification of larval life history traits of Syrphidae (Wong et al., 2023).Subterranean larval development has evolved across several Syrphidae lineages, with resource exploitation observed both in plant roots and root aphids (Speight, 2017;Wong et al., 2023).The phytosaprophagous larvae of Cheilosia impressa develop by feeding on the underground parts of its host plants, which is primarily Greater Burdock, Arctium lappa (Schmid, 1999).The two flight periods of C. impressa (May/July and August/September) may be partially univoltine rather than bivoltine, as Schmid (1999) observed 75% of larvae developed without diapause, while the remainder hibernated.
We hope that this novel high-quality sequenced genome of Cheilosia impressa, generated as part of the Darwin Tree of Life project, will help further understanding into the evolutionary biology and ecology of this unique species.

Genome sequence report
The genome was sequenced from one male Cheilosia impressa (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 37-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 8 missing joins or mis-joins, reducing the scaffold number by 7.81%, and increasing the scaffold N50 by 10.96%. The final assembly has a total length of 395.0 Mb in 58 sequence scaffolds with a scaffold N50 of 60.0 Mb (Table 1).
The snailplot in Figure 2 provides a summary of the assembly statistics, 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 (96.79%) 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 5; Table 2).The X chromosome was identified based on coverage, but no Y chromosome was identified.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.
The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the idCheImpr3 sample was weighed and dissected on dry ice (Jay et al., 2023).Tissue from the thorax was homogenised using a PowerMasher II tissue disruptor (Denton et al., 2023a).HMW  DNA was extracted using the Automated MagAttract v1 protocol (Oatley et al., 2023).The DNA was then sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30 (Todorovic et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation (Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory are available on protocols.io(Denton et al., 2023b).

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from head tissue of idCheImpr3 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.the final mitochondrial contig and to ensure the general quality of the sequence.
Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The 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.
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

Jerome H L Hui
The Chinese University of Hong Kong, Hong Kong, Hong Kong In this Data Note, Falk and colleagues sequenced and assembled the genome of hoverfly Cheilosia impressa (Loew, 1840).Occurrence of this species has been recorded in England, Wales and Scotland.Molecular data of this species are scarce prior to this report, and are mainly mitochondrial cytochrome c oxidase subunit I (COI) gene sequences deposited to the NCBI database.Therefore, this new genome resource will be useful for further studies, ranging from insect-plant interaction, its population structure, and their evolution with other insects.
This genome resource is excellent from the summary statistics, with high BUSCO number scores, high sequence continuity, and majority of sequences contained on the 5 pseudochromosomes (plus sex chromosome and mitochondrion).All in all, this is another valuable contribution.

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: I have published with Peter Holland more than three years ago, and confirm that this potential conflict of interest did not affect my ability to write an objective and unbiased review of the article.
Reviewer Expertise: Genomics, evolution, invertebrates Falk, Poole and colleagues describe a high-quality chromosome-level assembly of the hoverfly Cheilosia impressa produced following protocols, workflows and reporting templates developed by the DToL consortium.The resulting assembly has excellent quality parameters and will be a useful community resource.

Minor comments
This is not the first DToL assembly report that I have seen with a k-mer completeness of 100% and I find this somewhat counter-intuitive when the report describes a primary assembly and also states that alt contigs are reported and desposited.The k-mer completeness is calculated as the fraction of reliable k-mers in the read set that are also found in the assembly.But I would expect that the primary assembly would show some degree of incompleteness due to kmers unique to the alt contigs.Or does the completeness consider both primary and alt contigs together (in which case this should be specified)?Abstract: "Most of the assembly is scaffolded…" I think it would be more informative to also state the percentage of the assembly that has been assigned to chromosomes in this short abstract.

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: Genomics Bioinformatics Evolution
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 Cheilosia impressa, idCheImpr3.1: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 394,967,364 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 (146,349,529 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (60,011,629 and 54,006,746 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/CAOIRA01/dataset/CAOIRA01/snail.

Figure 3 .
Figure 3. Genome assembly of Cheilosia impressa, idCheImpr3.1:BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOIRA01/dataset/CAOIRA01/blob.

Figure 4 .
Figure 4. Genome assembly of Cheilosia impressa, idCheImpr3.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOIRA01/dataset/CAOIRA01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Cheilosia impressa, idCheImpr3.1:Hi-C contact map of the idCheImpr3.1 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=cQMzy7g9Qxa2TiZnHGNbgg.

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