The genome sequence of a hoverfly, Pocota personata (Harris, 1780)

We present a genome assembly from an individual male Pocota personata (a hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 845.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.04 kilobases in length.


Background
Pocota personata (Harris, 1780) is a European woodland hoverfly species, in the UK records are predominantly associated with wooded areas rich in dead and decaying trees in southern England, though it has been found as far north as North Yorkshire and County Durham (Ball & Morris, 2000;Ball & Morris, 2015;Stubbs & Falk, 2002;van Veen, 2014).It is described as a rare hoverfly throughout Europe with the majority of UK records existing between the months of April to August and a peak in numbers occurring during mid to late May (Ball & Morris, 2000;Ball & Morris, 2015;Stubbs & Falk, 2002).As larvae, P. personata are dark in colour and preferentially occupy elevated beech and poplar tree rot holes, activities relating to 'forest hygiene' including clearing of rotting logs and dead trees and filling of rot holes have been common practice in the past and may have impacted this species (Gandy, 2019;Rotheray, 1993;Stubbs & Falk, 2002).As adults P. personata are stocky bumblebee mimics, known for acoustic and behavioural mimicry through production of a distinctively loud buzz as well as repeated lifting of a hind leg if disturbed (Ball & Morris, 2015;Gandy, 2019;Stubbs & Falk, 2002).Adults possess two unique recognisable features setting them aside from other Syrphid bumblebee mimics, firstly a disproportionately small head, measuring approximately half the thorax width and additionally the presence of prominent bright yellow hairs on the thorax and abdomen (Ball & Morris, 2015).Flower visitation appears to be an occasional behaviour in P. personata, though it has been spotted visiting umbellifers, hawthorn and apple trees during the late afternoon and early evening (Ball & Morris, 2015;Stubbs & Falk, 2002).The completed genome sequence for Pocota personata is an important resource in aiding the future study of this scarce and poorly understood hoverfly species.

Genome sequence report
The genome was sequenced from one male Pocota personata (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.76,.A total of 30-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 108 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 22.22%, and increasing the scaffold N50 by 158.88%. The final assembly has a total length of 845.2 Mb in 265 sequence scaffolds with a scaffold N50 of 247.6 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 (98.27%) of the assembly sequence was assigned to 5 chromosomal-level scaffolds, 4 autosomes and the X sex chromosome.Chromosome X was identified by read coverage statistics.No Y was identified.The species is thought to be XO.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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.

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.
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 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 Table 3. Software tools: versions and sources.

Software tool Version
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

Pablo Aguado-Aranda
University of Alicante, Alicante, Spain First of all, I would like to congratulate the authors of this publication for their contribution to this topic.Special mention should be made of the background section which summarises the most relevant data on the species under study, my compliments to the authors.
My comments on this manuscript are simply suggestions and small changes.For example, I would recommend adding the authorship of the species also in the abstract.Regarding the methodology, I should avoid repeating information on data collection (locality, coordinates and date) of the specimen, as it is mentioned twice in the text: (1) at the beginning of the section "Genome sequence report" and (2) in the subsection "Sample acquisition and nucleic acid extraction".Regarding this subsection, I would recommend replacing the links to the reference of each of the protocols and referencing them in the text as the rest of the references.
Finally, as in previous reviews, as a reviewer I would like to point out that my knowledge and experience in whole genome sequencing procedures is very limited.Therefore, I suggest the editorial team to take this into account and consider other researchers with more experience in these topics for the review of this part.

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 Falk, Woodcock and colleagues report the sequencing and assembly of the genome of the hoverfly, Pocota personata.The genomic resources produced are high quality and will be of value to the scientific community.The assembly and report follow carefully developed DToL workflows and templates and these comprehensively capture metadata for software versions and assembly properties.
I have just minor questions/comments (the second of which I have also noted in a another report I have very recently reviewed).
(1) The intra-chromosome signals on contact map are relatively weak (compared to "typical" plots).Are there biological or technical reasons why this might be the case?
(2) Can I query the bead ratio stated in the methods "In brief, the method uses a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA."In my understanding, and from the guidelines on protocol.io,to eliminate smaller fragments, a lower ratio of beads to sample would be used.Should this be 0.6x?
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 A male Pocota personata (specimen ID Ox001535, ToLID idPocPers1) was netted in Wytham Woods, Oxfordshire (biological vice-country Berkshire), UK (latitude 51.76, longitude -1.33) on 2021-05-31.The specimen was collected and identified by Steven Falk (University of Oxford) and preserved on dry ice.High molecular weight (HMW) DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI), following a sequence of core procedures: sample preparation; sample homogenisation; HMW DNA extraction; DNA fragmentation; and DNA clean-up.The idPocPers1sample was weighed

Figure 2 .
Figure 2. Genome assembly of Pocota personata, idPocPers1.1: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 845,253,571 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 (279,389,706 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (247,560,496 and 123,742,089 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/Pocota%20personata/dataset/CAUJBT01/snail.

Figure 5 .
Figure 5. Genome assembly of Pocota personata, idPocPers1.1:Hi-C contact map of the idPocPers1.1 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=Ikse1PuTTceSUbllW6lsUQ.

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Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).
Sheared DNA was purified using Manual solid-phase reversible immobilisation (SPRI) (protocol at https://dx.doi.org/10.17504/protocols.io.kxygx3y1dg8j/v1).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