The genome sequence of an ichneumonid wasp, Campoletis raptor (Zetterstedt, 1838)

We present a genome assembly from an individual female Campoletis raptor (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 218.6 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.53 kilobases in length.

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Background
Campoletis raptor is a small (5-8 mm body length), largely black ichneumonid wasp with the metasoma mostly red medially, and with the hind tibia banded black and pale red.The ovipositor is relatively long and apically strongly upcurved.As with most species of Campoletis, the clypeus (below the face) has a median point.Campopleginae genera can be difficult to identify, although Klopfstein et al. (2022) have produced an interactive key to European genera.Riedel (2017) has revised the European species of Campoletis, with identification keys.The nominate subspecies of C. raptor ranges from Spain and the UK in the West to Bulgaria in the East, with a separate subspecies described for populations in Central Asia, in Kyrgyzstan and Turkmenistan (Riedel, 2017).Very little is known about the distribution of C. raptor in Britain or Ireland, although there are museum specimens from England.
As with most species of the ichneumonid subfamily Campopleginae, C. raptor is a koinobiont endoparasitoid of Lepidoptera larvae.Oviposition is into a small larva which is killed in a later instar, with the wasp larva spinning a cocoon outside the host remains.A variety of lepidopteran hosts have been reported for C. raptor, but these are mostly dubious because of potential parasitoid misidentifications.Riedel (2017), in his recent taxonomic revision, only reported Mythimna conigera (Denis & Schiffermüller) (Brown-line Bright-eye) as a host, although it is likely other hosts are attacked too.Campoletis species often have distinctively patterned, black and white cocoons, presumably mimicking bird droppings to offer some defence as they pupate in relatively exposed positions, with the host larva killed before it is fully grown (Broad et al., 2018).
Although little is known of the biology of C. raptor, the North American Campoletis sonorensis (Cameron) has been intensively studied as it is an important natural enemy of an agricultural pest caterpillar, Spodoptera frugiperda (Smith) (Isenhour, 1985;Isenhour, 1986).Campoletis sonorensis has a high fecundity and, as with other Campoletis species, pupation time in the cocoon can be rapid.Polydnaviruses are incorporated into the genome of C. sonorensis, helping the wasp larva overcome the host immune system (Federici & Bigot, 2003).As more genomes of polydnavirus-carrying wasps are assembled, from congenerics to more distantly related subfamilies, we will gain greater understanding of the roles these viruses have played in the diversification of parasitoids.

Genome sequence report
The genome was sequenced from one female Campoletis raptor collected from Wytham Woods, Oxfordshire (51.77,.
A total of 83-fold coverage in Pacific Biosciences singlemolecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 16 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the assembly length by 0.97% and the scaffold number by 19.23%, and increasing the scaffold N50 by 2.46%.
The final assembly has a total length of 218.6 Mb in 20 sequence scaffolds with a scaffold N50 of 18.6 Mb (Table 1).Most (99.98%) of the assembly sequence was assigned to 11 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 1-Figure 4; 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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/2922060.

Sample acquisition and nucleic acid extraction
A female Campoletis raptor (specimen ID NHMUK014451738, individual iyCamRapt1) was collected using an aerial net in Bert's Pheasant Pen, Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.31) on 2021-09-02.The collectors were Gavin Broad, Chris Fletcher and Inez Januszczak (all Natural History Museum).The specimen was identified by Gavin Broad (Natural History Museum) and then dry frozen (-80°C).
The specimen was prepared for DNA extraction at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyCamRapt1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Whole organism tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.DNA was extracted at the Wellcome Sanger Institute (WSI) Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.

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 the Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from tissue of iyCamRapt1 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.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  (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 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  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.
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The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material • Legality of collection, transfer and use (national and international) and in some circumstances other Darwin Tree of Life collaborators.

Open Peer Review
Current Peer Review Status:

Marko Prous
Museum of Natural History, University of Tartu, Tartu, Estonia The paper presents a genome sequence of Campoletis raptor (Ichneumonidae).The standard Darwin Tree of Life Consortium methods have been used.Seems that most or all the relevant papers have been cited to enable replication of the results more or less.Because of probably inevitable manual intervention during some of steps, genome assembly is difficult to standardize in general.
I liked the background section providing main information about the organism (taxonomy, biology...), which is valuable addition to the genome report.
In summary I don't have any specific criticism of the paper.My general suggestion would be to combine in the future at least some of the genome reports into one paper, combining based on taxonomic group or some other interesting aspect.Then there could be at least one additional aspect to that could make the paper more interesting and relevant.For example in case of Ichneumonidae or Ichneumonoidea a small comparative aspect of polydnaviruses in their genomes could be nice addition to standard genome reports.This could also make finding reviewers for the papers easier (fewer and more more interesting papers).

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? Partly
Are the datasets clearly presented in a useable and accessible format?Yes

Željko Tomanović
Serbia University of Belgrade, Belgrade, Serbia The genome sequence of Campoletis raptor was presented by the authors.Although the biology of this species is not well known, the authors pointed out importance of the related North American Campoletis sonorensis, which is a natural enemy of Spodoptera frugiperda.The authors provided sufficient background information on these taxa and presented the genome of C. raptor in appropriate way.

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: Taxonomy, Phylogenetics, biodiversity 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 1 .
Figure 1.Genome assembly of Campoletis raptor, iyCamRapt1.1: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 218,627,199 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 (38,199,786 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,621,092 and 12,881,085 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/iyCamRapt1.1/dataset/CANUFJ01/snail.
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

Figure 2 .
Figure 2. Genome assembly of Campoletis raptor, iyCamRapt1.1: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/iyCamRapt1.1/dataset/CANUFJ01/blob.

Figure 3 .
Figure 3. Genome assembly of Campoletis raptor, iyCamRapt1.1: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/iyCamRapt1.1/dataset/CANUFJ01/ cumulative.

Table 1 . Genome data for Campoletis raptor, iyCamRapt1.1. Project accession data
(Allio et al., 2020)tochondrial genome was assembled using MitoHiFi(Uliano-Silva et al., 2022), which runs MitoFinder(Allio et al., 2020)or MITOS 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.