The genome sequence of the common buff snailkiller, Tetanocera ferruginea (Fallén, 1820)

We present a genome assembly from an individual male Tetanocera ferruginea (the common buff snailkiller; Arthropoda; Insecta; Diptera; Sciomyzidae). The genome sequence is 790.4 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 17.07 kilobases in length.


Background
Since the seminal discovery of obligate malacophagy (mollusc-feeding) in the dipteran family Sciomyzidae by (Berg, 1953), there has been a steady increase in our knowledge of the family (Berg & Knutson, 1978;Murphy et al., 2012), so that today, lifecycles are known in 203 species out of a total described number of species of 539 (38% of the family) making Sciomyzidae among the most biologically well-known dipterous families in the world (Knutson & Vala, 2011).Tetanocera ferruginea Fallén, 1820 is a medium to large fly, rather drab in colour being light brown with no obvious wing markings other than those common to all Tetanocera species.It is not easily distinguished from Tetanocera fuscinervis (Zetterstedt, 1838) or other Tetanocera species.It has shorter legs than Tetanocera hyalipennis von Roser, 1840, is smaller than Tetanocera robusta Loew, 1847, but reliable identification requires dissection of male genitalia.Good figures of male postabdomen morphology are given in Rozkošný (1984), Rozkošný (1987) and Vala (1989).Naturhistoriska Riksmuseet, Stockholm, Sweden held the holotype, but it is presumed lost (Vala et al., 2012).
Tetanocera ferruginea has a Holarctic distribution (Vala et al., 2012) with distribution maps provided in Foote (1999), Sueyoshi (2001), Williams et al. (2007) and McDonnell et al. (2010).It is not considered scarce or threatened in the UK (Falk, 1991).The biology of T. ferruginea is discussed in some detail in Foote (1961), Rozkošný (1965), andVala (1989).It was placed in Phenological Group 1 by Berg et al. (1982).This Group is defined as follows: "Multivoltine species overwintering in the puparium as diapausing or quiescent prepupae, pupae, or pharate adults.The puparial stage is found throughout the year" (Vala et al., 2012).Knutson and Vala (2011) placed T. ferruginea in Behavioural Group 11.This Group is defined as follows: "Predators of non-operculate snails at or just below the water surface, just above the surface on emergent vegetation, and occasionally on snails exposed on moist, 'shoreline' surfaces" (Vala et al., 2012).It has been shown to have very limited movements within habitats despite large populations (Williams et al., 2010) This genome sequence will be extremely useful for applying Rad-Seq analysis to the population genetics of T. ferruginea, as suggested by Williams (2023).Previous population genetics studies of Sciomyzidae are limited to a 1990 isozyme study of the Sepedon fuscipennis group (Manguin, 1990).More recent population genetics work has attempted to study Tetanocera ferruginea but failed to produce sufficient specimens.It is not clear yet whether this is due to a general global decline in the species or a temporary bottleneck.

Genome sequence report
The genome was sequenced from one male Tetanocera ferruginea (Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), 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 87 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the scaffold number by 31.4%, and increasing the scaffold N50 by 19.24%. The final assembly has a total length of 790.4 Mb in 82 sequence scaffolds with a scaffold N50 of 161.6 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 (99.18%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds, representing 5 autosomes and the X and Y sex chromosomes.The sex chromosomes were determined by coverage statistics and synteny to Pherbina coryleti (GCA_943735915.1)(Sivell et al., 2023) and Coremacera marginata (GCA_914767935.1)(Sivell et al., 2021).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 estimated Quality Value (QV) of the final assembly is 57.2 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 97.7% (single = 96.8%,Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/ 320963.idTetFerr1 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 pestle (https://dx.doi.org/10.17504/protocols.io.5qpvo3r19v4o/v1).DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.

Sample acquisition and nucleic acid extraction
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 DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific   ( 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 which they have been/are to be collected and provided for Table 3. Software tools: versions and sources.

Software tool Version
Operations core at the WSI on a Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from remaining tissue of idTetFerr1 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).

Darren J Obbard
The University of Edinburgh, Edinburgh, Scotland, UK This data note reports the sequencing and assembly of the genome of Tetanocera ferruginea as part of the "Darwin Tree of Life" programme.In common with other data notes from this research effort, the reporting is standardised and quite brief.As such, I have very few comments to make.
The approach is state-of-the-art, the raw data appear to be of a suitably high quality, and the assembly methods are appropriate.The public availability of raw data and genome assembly are appropriate.The resulting genome is likely to be of very high quality, and I have no doubt that it will be of great value to any researchers working on this group of flies, or on the comparative or evolutionary genomics of insects more generally.
My suggestions for improvement all pertain to the writing of the text, which is sometimes oddly structured and hard to read.It would be nice if the article included a better (live, habitus) picture, in addition to the one of the sequenced specimen.○ Writing Structure: "The biology of T. ferruginea is discussed in some detail in … " -it would be useful to provide a 1-3 sentence summary of this biology here, citing those references.

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Writing Structure: "This Group is defined as follows: …" I do not feel it is appropriate to quote previous papers in this way.The information should be synthesised / summarised here for the reader.

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In addition, I think the note would benefit from further links to the research literature (see reference below).

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In general, more explicit information on the ecological, temporal, and host range in the would be appreciated.Reviewer Expertise: Metagenomics, genomics, phylogenetics, and population genetics of invertebrates and their parasites.
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 Tetanocera ferruginea, idTetFerr1.1: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 790,383,743 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 (172,084,289 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (161,584,466 and 133,911,736 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/Tetanocera%20ferruginea/dataset/idTetFerr1_1/snail.
A male Tetanocera ferruginea (specimen ID Ox002718, ToLID idTetFerr1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude -1.34) on 2022-06-14.The specimen was collected by Liam Crowley (University of Oxford) and Steven Falk (independent researcher) and identified by Steven Falk 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

Figure 3 .
Figure 3. Genome assembly of Tetanocera ferruginea, idTetFerr1.1: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/Tetanocera%20ferruginea/dataset/idTetFerr1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Tetanocera ferruginea, idTetFerr1.1: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/Tetanocera%20ferruginea/dataset/idTetFerr1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Tetanocera ferruginea, idTetFerr1.1:Hi-C contact map of the idTetFerr1.1 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=BnOn57OCRVWnD40LgRLOKg.

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First line: "… in the dipteran family Sciomyzidae by(Berg, 1953) …" should be formatted as "… in the dipteran family Sciomyzidae by Berg (1953) …" ○ It might be nice to mention that this appears to be one of the species cited as an example byBerg (1953), ○ At 75 words, the first sentence is unusually long and hard to read.
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.

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:
(Allio et al., 2020), 2023)e mitochondrial genome was assembled using MitoHiFi(Uliano-Silva et al., 2023), which runs MitoFinder(Allio et al., 2020)or MITOS 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: No competing interests were disclosed.
Minor editorial points: 1.The narrative cites specific work with the authors in and outside parentheses.Examples: Sciomyzidae by (Berg, 1953),... provided in Foote (1999),...The manuscript could be looked over for consistency.2."More recent population genetics work has attempted to study Tetanocera ferruginea but failed to produce sufficient specimens."Personal observation by the authors?If so, state in parentheses.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
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.