The genome sequence of the bulrush Neoascia, Neoascia interrupta (Meigen, 1822)

We present a genome assembly from an individual female Neoascia interrupta (the bulrush Neoascia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 601.9 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 17.76 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,086 protein coding genes.


Background
The bulrush Neoascia, Neoascia interrupta (Meigen, 1822), is a predominantly black and notably small species of hoverfly found in Northern and Central Europe and Western Siberia (van Veen, 2014).In the UK N. interrupta are found between the months of April and September and peak in numbers during June (Stubbs & Falk, 2002).After a relatively recent addition to the UK species list in 1981, records of N. interrupta are most frequent in the East of England though individuals have been documented across Southern England, Wales and into South Yorkshire (Ball & Morris, 2000;Ball & Morris, 2015).Adults display a preference for vegetation surrounding ponds, marshes, ditches and canals which are often rich in bulrush reeds, hence their common name, the bulrush Neoascia (Stubbs & Falk, 2002).The species has additionally been noted occupying semi-brackish ditches in coastal areas of Kent and Essex (Stubbs & Falk, 2002).N. interrupta is distinguished from other Neoascia hoverflies by the presence of yellow spots on the edges of abdominal tergite 4, which are lacking in other members of the genus (Stubbs & Falk, 2002;van Veen, 2014).Females have a club-shaped lower abdomen, contrastingly males are more streamlined in appearance, though both sexes are noted for their distinct wasp-like narrow waists (Ball & Morris, 2015).Species specific records of breeding and larval development are limited, though larvae of the Neoascia genus have been found in wet manure, compost and decaying vegetation associated with the banks of ponds and ditches (Ball & Morris, 2015;Rotheray, 1993).Adult N. interrupta are frequent flower visitors and can be spotted flying slowly among low-growing flowers such as forget-me-nots and fool's watercress (Stubbs & Falk, 2002;van Veen, 2014).The completed genome sequence for Neoascia interrupta as part of the Darwin Tree of Life Project provides the opportunity to further investigate this understudied hoverfly species.

Genome sequence report
The genome was sequenced from one female Neoascia interrupta (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.76,.A total of 45-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 134 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 60.61%, and increasing the scaffold N50 by 14.82%. The final assembly has a total length of 601.9 Mb in 38 sequence scaffolds with a scaffold N50 of 219.1 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 (99.17%) of the assembly sequence was assigned to 4 chromosomal-level scaffolds, representing 3 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).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 resulting annotation includes 22,574 transcribed mRNAs from 22,086 protein-coding genes.

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 tissue of idNeoInte1 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   Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Neoascia interrupta assembly (GCA_947623515.1) in Ensembl Rapid Release.

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.

Software tool Version
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

Main
This Genome note provided a high-quality sequence dataset, and it contributes to the global resources for future discoveries by the scientific community.Minor I think that the authors could give more context about the importance (economic or social aspect) of this species, beyond that mentioned in the Introduction section.
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.

Figure 2 .
Figure 2. Genome assembly of Neoascia interrupta, idNeoInte1.1: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 601,923,271 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 (226,676,804 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (219,059,534 and 128,085,943 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/Neoascia%20interrupta/dataset/CANQKQ01/snail.

Figure 5 .
Figure 5. Genome assembly of Neoascia interrupta, idNeoInte1.1:Hi-C contact map of the idNeoInte1.1 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=LMw6NIp_REaXbeYMTvjmaw.

©
2024 Diambra L. 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.Luis DiambraUniveridad Nacional de La Plata, La Plata, Argentina This manuscript from Falk and Woodcock reports the genome of an individual female of Neoascia interrupta.Raw genomic data was generated by Pacific Biosciences single-molecule HiFi.These long reads were assembled and scaffolded to Hi-C data.Haplotypic duplication was manually removed.The authors provide the assembly statistics obtained by using BlobToolKit Snailplo.The genome annotation was performed by BRAKER2 pipeline and includes 22,574 transcripts and 22,086 protein-coding genes.All these analyses are clearly explained in the protocols of Tree of Life laboratory which contains enough information to allow replication by other researchers.

Table 1 . Genome data for Neoascia interrupta, idNeoInte1.1. Project accession data
* Assembly metric benchmarks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).** BUSCO scores based on the diptera_odb10 BUSCO set using v5.3.2.C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison.A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Neoascia%20interrupta/dataset/CANQKQ01/busco. by Steven Falk (University of Oxford) and preserved on dry ice.The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation; DNA extraction; HMW DNA fragmentation; and fragmented DNA clean-up.The sample was prepared for DNA extraction at the WSI Tree of Life laboratory: the dNe-oInte1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing (https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1).Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher

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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
Reviewer Report 13 March 2024 https://doi.org/10.21956/wellcomeopenres.22538.r73549