The genome sequence of the Figwort Cheilosia, Cheilosia variabilis (Panzer, 1798)

We present a genome assembly from an individual male Cheilosia variabilis (the Figwort Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 414.7 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.77 kilobases in length.


Background
Cheilosia is the most speciose hoverfly genus in Europe, however, because its species are mostly black and lack any obvious defining features, they are notoriously difficult to identify and often overlooked as hoverflies (Vujic et al., 2013).Members of the Cheilosiini tribe share a defined margin between the eye and the face called a 'zygoma'.C. variabilis belongs to a small group of Cheilosia that possess distinctive uptstanding hairs between the zygoma and the central facial knob (Ball & Morris, 2013;van Veen, 2010).
The Figwort Cheilosia, Cheilosia variabilis, is a large, black hoverfly with particularly long wings (wing length 7.75-10.25mm) common throughout the Palearctic realm (Ball & Morris, 2013).This species is frequently observed along woodland rides in deciduous forests, feeding on white umbellifers and settling on foliage with its wings held in a characteristic delta shape posture (Speight, 2017;van Veen, 2010).C. variabilis are bivoltine, producing two broods of offspring per year during their flight period of April to September (Speight, 2017).The larvae are phytophagous and bore into the rhizomes of the Common Figwort, Scrophularia nodosa, and the stalks of the Water Figwort, S. auriculata, hence its common name (Coe, 1953;Dušek, 1962;Rotheray, 1990;Rotheray & Gilbert, 1999).
The distribution of the Figwort Cheilosia spans from Ireland to Western Siberia and Iran, and from Fennoscandia to Morocco, and it is also widespread across the United Kingdom (Khaganinia & Kazerani, 2014).This species' range and abundance across the Balkan Peninsula is predicted to decrease under current climate projections, highlighting their dependence on the cooler, more humid habitats found at the lower elevations of this vast mountainous region (Radenković et al., 2017).It is anticipated that this novel high-quality sequenced genome of Cheilosia variabilis, generated as part of the Darwin Tree of Life project, will help progress an understanding into this species' biology and ecology.

Genome sequence report
The genome was sequenced from one male Cheilosia variabilis (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 63-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 26 missing joins or misjoins and removed one haplotypic duplication, reducing the scaffold number by 66.67%, and increasing the scaffold N50 by 7.12%. The final assembly has a total length of 414.7 Mb in 7 sequence scaffolds with a scaffold N50 of 70.7 Mb (Table 1).Most (99.99%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds, 5 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).The X and Y chromosomes were identified by read coverage.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/273447.

Sample acquisition and nucleic acid extraction
A male Cheilosia variabilis (specimen ID Ox002181, individual idCheVari2) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.33) on 2022-05-19 by netting.The specimen was collected and identified by Liam Crowley (University of Oxford).The specimen used to generate Hi-C data (specimen ID NHMUK014452799, ToLID idChe-Vari1) was collected from the Eden Project, Cornwall (latitude 50.36, longitude -4.74) on 2021-06-28.This specimen was collected by Olga Sivell (Natural History Museum) and identified by Michael Ashworth (independent researcher).Both specimens were preserved on dry ice.
The idCheVari2 sample was prepared for DNA extraction at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The sample was weighed and dissected on dry ice.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.

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 (HiFi) instrument.Hi-C data were also generated from head and thorax tissue of idCheVari1 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., 2023), 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  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     This data-note is ok: the genome data is great, clearly presented, the reading is smooth.So my "review" is necessarily positive.
I noticed however that figures are quite "raw".Indeed, I inspected other data-notes from the same journal and I noticed that it is basically the same type of figures likely auto-generated by the pipeline.Therefore this type of note is just an exercise of writing 20 lines of introduction on an animal and copy and paste the pipeline output figures.Probably the most complicate part of the work is to reshuffle method's text in order to look like it is original and not a copy of previous (basically identical) text.I guess that the whole process can be automatically made by an AI.Fact is that another AI should review it, not a scientist.
All the best.

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. 1.
In the interest of reproducibility, it is advisable to create a GitHub (or similar) page containing the commands used and the entire pipeline used for genome assembly.This will facilitate transparency and accessibility for future researchers.

2.
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?Partly Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genomics, phylogenomics 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 variabilis, idCheVari2.1: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 414,757,870 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 (146,055,565 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (70,713,320 and 60,228,328 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/idCheVari2.1/dataset/idCheVari2_1/snail.

Figure 3 .
Figure 3. Genome assembly of Cheilosia variabilis, idCheVari2.1: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/idCheVari2.1/dataset/idCheVari2_1/blob.

Figure 4 .
Figure 4. Genome assembly of Cheilosia variabilis, idCheVari2.1: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/idCheVari2.1/dataset/idCheVari2_1/ cumulative.

Figure 5 .
Figure 5. Genome assembly of Cheilosia variabilis, idCheVari2.1:Hi-C contact map of the idCheVari2.1 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=JLVp73kbRgqOs5W3nRNJjw.