The genome sequence of the white-footed hoverfly, Platycheirus albimanus (Fabricius, 1781)

We present a genome assembly from an individual female Platycheirus albimanus (the white-footed hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 677.8 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,568 protein coding genes.


Background
Platycheirus albimanus (Fabricius, 1781), also referred to as the white-footed hoverfly, is one of the most familiar, widespread and abundant hoverflies across the UK and Ireland (Ball & Morris, 2000;Ball & Morris, 2015;Stubbs & Falk, 2002).Platycheirus is the second largest British hoverfly genus currently comprising 25 species.P. albimanus can be mistaken for other members of the genus including P. sticticus and P. discimanus.Consequently, use of a specialist key is often necessary to conclusively identify individuals to species level (Ball & Morris, 2000;Stubbs & Falk, 2002;van Veen, 2014).Adult female P. albimanus are identified through the presence and shape of silver-grey abdominal tergite spots, predominantly yellow legs and a faintly dusted face (Ball & Morris, 2015;Stubbs & Falk, 2002).In males, the colouring of tergite spots is usually bronze but sometimes appears grey or dull yellow.Males also have distinctive tangled hairs at the base of the front femur and a marked swelling at the apex of the front tibia (Stubbs & Falk, 2002;van Veen, 2014).
It is a relatively small hoverfly species often associated with brambles and nettles in woodland-edges, hedgerows and gardens (Ball & Morris, 2000;Stubbs & Falk, 2002).The species has multiple broods per season and can be found all year round with numbers peaking twice annually during May to June and July to August (Ball & Morris, 2015;Stubbs & Falk, 2002).The larvae of P. albimanus are aphid predators and have been observed among low-growing foliage as well as on fir trees and common reeds (Stubbs & Falk, 2002).
Generation of a reference genome for Platycheirus albimanus provides a valuable tool to further the knowledge of this prominent UK hoverfly species.Here we present a chromosomally complete genome sequence for Platycheirus albimanus, sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Genome sequence report
The genome was sequenced from one female Platycheirus albimanus (Figure 1) collected from Wytham woods, Oxfordshire, UK (51.77,.A total of 50-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 27-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 502 missing joins or mis-joins and removed 10 haplotypic duplications, reducing the assembly length by 1.22% and the scaffold number by 76.73%, and increasing the scaffold N50 by 363.49%. The final assembly has a total length of 677.8 Mb in 94 sequence scaffolds with a scaffold N50 of 375.7 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 (99.52%) of the assembly sequence was assigned to 4 chromosomal-level scaffolds, representing 3 autosomes and the X sex chromosome.The very large repetitive region of chromosome 1, spanning 119.95 Mb to 193.61 Mb is less certain than the rest of the assembly.It has been assembled to best fit the Hi-C data.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.
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.
The RNA concentration was 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 the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.
All wet lab protocols developed by the Tree of Life laboratory are publicly available on protocols.io:https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v1.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi), Illumina HiSeq 4000 (RNA-Seq) and HiSeq X Ten (10X) instruments.Hi-C data were also generated from abdomen tissue of idPlaAlba1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.scaffolded with Hi-C data (Rao et al., 2014) using SALSA2 (Ghurye et al., 2019).The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) andPretext (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.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Platycheirus albimanus assembly (GCA_916050605.2).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

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

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: Bioinformatics
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.Another suggestion is to provide information about the expected genome size and the size obtained, as well as the number of chromosomes, possibly drawing comparisons with closely related species.
In conclusion, this is an excellent genome assembly, and these few adjustments would further enhance the description of this species and contribute valuable knowledge to the scientific community.I appreciate the initiative's commitment to open data.

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: I work on the genome of plant-parasitic nematodes from the genus Meloidogyne.I have assembled and helped on the genome of different species of plant parasitic nematodes, which have a complex allopolyploid genome.
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, however I have significant reservations, as outlined above.
Reviewer Reviewer Expertise: I focus on the phylogeny and evolution of insects, especially on grasshoppers.Since 2016, I have personally helped generate several genome sequences across a diverse array of insect species.Through this long-term involvement, I have developed a thorough understanding of the methodological approaches, bioinformatic workflows, and computational techniques employed in whole genome projects.
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 Platycheirus albimanus, idPlaAlba1.2: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 677,786,980 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 (375,708,846 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (375,708,846 and 116,005,501 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/Platycheirus%20albimanus/dataset/CAJZLR02/snail.

Figure 5 .
Figure 5. Genome assembly of Platycheirus albimanus, idPlaAlba1.2:Hi-C contact map of the idPlaAlba1.2assembly, 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=OqJMIWx0Rg6Wz0yJDVxuZw.

©
2024 Mota A. 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.Ana Paula Zotta Mota Institut Sophia Agrobiotech, INRAE, CNRS, University of Côte d'Azur, Nice, Provence-Alpes-Côte d'Azur, FranceThe Darwin Tree of Life initiative and the production of high-quality genome assemblies represent a crucial first step towards gaining a deeper understanding of evolutionary processes.The data presented in this paper are excellent, demonstrating high coverage of the genome and exceptional data quality.The methods used are sound and appropriate for the type of data and the results obtained.I have a few suggestions that could further enhance the findings.In the Hi-C map, the boundaries between chromosomes are not clearly visible.The authors might consider adjusting the resolution or color scale based on previous feedback to improve visibility.Additionally, I wonder if the authors have searched for canonical telomeric sequences (TTAGGG) within their genome assembly.Highlighting these sequences and their positions on the Hi-C map, perhaps using a wig file to indicate the locations of these telomeric repeats, could be very informative.This addition would complement the already impressive results and provide clearer insights into chromosome organization.
Report 01 March 2024 https://doi.org/10.21956/wellcomeopenres.22687.r74297© 2024 Guan D. 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.De-Long GuanShaanxi Normal University, Xi'an, Shaanxi, China I am glad to see your article on the genome assembly of Platycheirus albimanus.I appreciate the time and effort you put into this work.Genome sequencing is crucial for advancing our scientific understanding, and projects like yours are helping to make whole genome data more accessible.Overall, I found your manuscript to be well written and the methods sound.I was able to follow your assembly and annotation processes without difficulty.The quality of assembly you achieved is impressive, especially the level of chromosomal scaffolding.I also thought the figures were welldesigned to highlight the key results.One small point of feedback relates to the HiC contact map figure.While the overall contacts between scaffolds are clear, I had a little trouble distinguishing the individual chromosomes due to the density of interactions shown.A potential way to address this could be adjusting the resolution or color scale to better delineate each pseudomolecule.In closing, I believe this genome will serve as a valuable reference for future research on P. albimanus and Dipteran insects more broadly.Please address the minor comment above as you are able.Subject to satisfactory revision.Thank you again for your contribution to open data.Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.