The genome sequence of an ichneumonid wasp, Oxytorus armatus Thomson, 1883

We present a genome assembly from an individual male Oxytorus armatus (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 367.8 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 56.22 kilobases in length.


Background
Oxytorus armatus is a widespread ichneumonid wasp.Females are rather distinctive as they have white-striped antennae, small projections on the propodeum (apophyses), a long and posteriorly compressed metasoma (the abdomen beyond the first segment), and short, wide ovipositor sheaths.The only other European (including British) species of Oxytorus, O. luridator, can be separated most easily by its much smaller apophyses, closed areolet in the fore wing, and shorter metasoma.Males are very similar but can usually be separated by the absence of the areolet in O. armatus and the rougher, more 'leathery' sculpture on the second metasomal tergite.Kerrich (1939) and van Rossem (1987) provide some notes on identification.The main problem in identifying males of Oxytorus is in recognising that they are oxytorines.The subfamily Oxytorinae comprises the single genus Oxytorus, which is defined by some distinctive features such as the female metasoma shape, the flattened clypeus and the exceptionally long maxillary palps.Males, however, look rather indistinct and are often passed over as specimens of Ctenopelmatinae, Cryptinae or Phygadeuontinae.
Based on specimens in museum collections, especially light-trapped individuals identified by GRB, adults are active from June to early September, most commonly in June and July.Oxytorus armatus has a wide range across Europe, as does O. luridator, although O. luridator is perhaps the more commonly collected of the two.Usually found in deciduous woodland, we know very little about the ecology of O. armatus.As with O. luridator, males are frequently attracted to light so are presumably at least partly nocturnal or crepuscular.In fact, the small subfamily Oxytorinae is one of only three ichneumonid subfamilies entirely lacking host records.Oxytorinae is the most species-rich of those three, with 25 described species and several undescribed species found across both temperate and tropical areas of Asia, Europe and the Americas (Broad et al., 2018;Riedel et al., 2021).As pointed out by Wahl (1990), when classifying Oxytorus in their own subfamily, the short ovipositor of Oxytorus has a subapical notch, which means they will be endoparasitoids of larvae.
In the few large-scale phylogenetic studies which have included Oxytorus (Bennett et al., 2019;Quicke et al., 2009;Sharanowski et al., 2021), they have been found to be part of a grouping called the 'ophioniformes', and part of a very large clade which are invariably koinobiont endoparasitoids of holometabolous insect larvae, i.e., the host develops further following oviposition, with the wasp larva feeding internally.
Oxytorus might be closely related to some of the groups of sawfly parasitoids currently classified as Ctenopelmatinae, which are not monophyletic Oxytorus (Bennett et al., 2019;Quicke et al., 2009;Sharanowski et al., 2021), but are all parasitoids of sawfly (Hymenoptera) larvae.It is conceivable that Oxytorus will be found to be parasitoids of sawfly larvae, but it is striking that while the larvae of many northern European sawfly species have been reared, Oxytorus never has.The metasoma adaptations, and the fact that females seem to stay near ground level (Broad et al., 2018) suggests that the hosts will be concealed in loose, or easily penetrated substrate.The availability of a genome will help to pin down the affinities of this enigmatic group of Darwin Wasps, and hopefully spur efforts to rear these wasps.

Genome sequence report
The genome was sequenced from one male Oxytorus armatus (Figure 1) collected from Bert's Pheasant Pen, Wytham Woods, Oxfordshire, UK (51.77,.A total of 62-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 35 missing joins or mis-joins, reducing the scaffold number by 26.42%, and increasing the scaffold N50 by 0.66%. The final assembly has a total length of 367.8 Mb in 38 sequence scaffolds with a scaffold N50 of 31.2Mb (Table 1).The snail plot 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 (99.98%) of the assembly sequence was assigned to 13 chromosomal-level scaffolds.The genome is of a haploid male specimen.Chromosomescale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol (Oatley et al., 2023).The DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31  tissue of iyOxyArmt1 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).
Table 3 contains a list of relevant software tool versions and sources.

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Software tool Version
The study presented a chromosome-level genome assembly for a widespread ichneumonid wasp, Oxytorus armatus, using genomic DNAs obtained from one single male.The genome sequence is 367.8Mb in length, with 13 chromosomal pseudomolecules.The Method of this paper was clear and the Result was reliable.This reference genome will be useful in understanding the evolution and rearing of this wasp.

Juan Wulff
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA The work in general is very good and the method used for sequencing is quite robust.The manuscript is short, but I understand that it is more of a report or short communication than a research paper.This is my fourth time reviewing this type of work for this journal and I always mention the same thing, especially since they are all almost identical, the main weakness of these studies is that the annotation was done using a database without transcriptomes to support gene annotation.However, I must say that given the large scale of this project, obtaining the genomes of closely related species will improve gene annotation.Likewise, the absence of species-specific isoforms will always be a weakness of this study and other similar ones that I have reviewed.
Finally, I think that the quality of the genome assembly is very good.

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: Biology, Entomology, Molecular biology and Genetics.
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 Oxytorus armatus, iyOxyArmt1.1:metrics.The BlobToolKit snail plot 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 367,853,913 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 (43,478,420 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (31,210,731 and 19,609,202 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 hymenoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/iyOxyArmt1_1/dataset/iyOxyArmt1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Oxytorus armatus, iyOxyArmt1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/iyOxyArmt1_1/dataset/iyOxyArmt1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Oxytorus armatus, iyOxyArmt1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/iyOxyArmt1_1/dataset/iyOxyArmt1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Oxytorus armatus, iyOxyArmt1.1:Hi-C contact map of the iyOxyArmt1.1 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=QG7ssJ0OSkGxmzq4ZBVN8A.

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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.

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