The genome sequence of an ichneumon wasp, Ophion slaviceki (Kriechbaumer, 1892)

We present a genome assembly from an individual female Ophion slaviceki (an ichneumon wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 654.2 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,399 protein coding genes.


Background
Ophion slaviceki is a widely distributed and often common ichneumonid (Darwin Wasp), a parasitoid wasp of the cosmopolitan subfamily Ophioninae.Like most ophionines, Ophion slaviceki is primarily nocturnal, seeking night-active caterpillars.It possesses numerous features associated with nocturnal behaviour, such as a uniformly pale reddish colour, long antennae, and very large compound eyes and ocelli (Gauld & Huddleston, 1976).
Ophion slaviceki is active almost exclusively in August and September, and is a parasitoid of Agrotis noctuid moths, particularly Heart and Dart (Agrotis exclamationis (Linnaeus, 1758)) and Turnip Moth (Agrotis segetum (Denis & Schiffermüller, 1775)) (Broad et al., 2015).The host larvae are well-grown at this time of year, emerging at night to feed on low vegetation.The Agrotis caterpillars feed periodically throughout winter and then form a pupation retreat in the soil in the spring.At this point, the O. slaviceki larva completes its feeding and emerges from the host to spin a densely woven, dark brown silken cocoon, from which the adult emerges later that year.As with its hosts, O.slaviceki seems to be very widespread across Britain and Ireland but distribution data are sparse (Broad et al., 2015).Adult O. slaviceki are separable from other similar Ophion species by a combination of a long trochantellus on the hind leg, mandibles with a simple, acutely angled gap between the teeth, and the fore wing venation, with a combination of a sinuous vein RS and a very short ramulus (Brock, 1982;Johansson & Cederberg, 2019).
In Britain, O. slaviceki is one of 31 Ophion species found so far, with more to be discovered.When the checklist of British and Irish Ichneumonidae was published in 2016 (Broad, 2016), only 16 species in the genus were recognised.Long known to be a taxonomically difficult genus, the use of DNA barcode data helped unravel various species complexes.Johansson and Cederberg (2019) overhauled the taxonomy of Swedish Ophion, with many of the newly described species present in the UK too.Ophion slaviceki has been called Ophion luteus (Linnaeus, 1758) in most publications, but the actual O. luteus is a smaller species which flies in early summer (Johansson & Cederberg, 2019).
The genome of O. slaviceki is the first chromosomal level genome for the subfamily Ophioninae, and one of a small number for the ophioniformes group of subfamilies (Wahl, 1991), a monophyletic group which is noteworthy for being koinobiont parasitoids (i.e., they allow their hosts to continue development following oviposition) and for repeated adoptions of viruses which have allowed these wasps to overcome host immune responses (Legeai et al., 2020).
Comparative genomics should illuminate some of the adaptations which have allowed these wasps to exploit host insects in such intricate ways.

Genome sequence report
The genome was sequenced from one female Ophion slaviceki (Figure 1) collected from Tonbridge, England, UK (50.25,1.64).A total of 35-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 56-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 1,749 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the scaffold number by 63.81%, and increasing the scaffold N50 by 23.11%.
The final assembly has a total length of 654.2 Mb in 571 sequence scaffolds with a scaffold N50 of 50.2 Mb (Table 1).Most (97.75%) of the assembly sequence was assigned to 13 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-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.

Sample acquisition and nucleic acid extraction
A female Ophion slaviceki (specimen IDNHMUK010635140, ToLIDiyOphLute1) was collected from a garden in Tonbridge, Kent (latitude50.25,longitude 1.64)on 2020-08-20 using a light trap.The specimen was collected and identified by Gavin Broad (Natural History Museum) and snap-frozen in liquid nitrogen.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyOphLute1 sample was weighed and dissected on dry ice with head and thorax tissue set aside for Hi-C sequencing.Tissue from the abdomen was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ngaliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.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.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (10X) instruments.Hi-C data were also generated from head and thorax tissue of iyOphLute1 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).One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes (Garrison & Marth, 2012).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.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Ophion slaviceki assembly (GCA_944452715.1) 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.
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  Table 3. Software tools: versions and sources.

Software tool Version
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

Elisabeth A Herniou
Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS -University of Tours, Tours, France This the report describing the complete genome sequence of the parasitoid wasp Ophion slaviceki.This species is part of a species complex which was recently revised.It parasitised important pest species from the lepidtoperan genus Agrotis.This chromosomal assembly prodives invaluable data for the comparative genomic investigation of Ichneumonid wasps.Reviewer Expertise: diversity, ecology, phylogeny parasitoid wasps 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 Ophion slaviceki, iyOphLute1.1: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 654,238,417 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 (75,994,433 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (50,234,018 and 33,763,864 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/iyOphLute1.1/dataset/CALYCA01/snail.

Figure 5 .
Figure 5. Genome assembly of Ophion slaviceki, iyOphLute1.1:Hi-C contact map of the iyOphLute1.1 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=Xdr6JEDrS4uD2QhUm0QmeQ.

©
2024 Tomanović Ž.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.Željko TomanovićSerbia University of Belgrade, Belgrade, SerbiaThe author presented the genome of a nocturnal ichneumon wasp, Ophion slaviceki, previously thought to be Ophion luteus.The article gave an excellent background with known biology and ecology of the sequenced specimen.Technically and methodologically the article contains sufficient explanation and looks very good.The article is very well written.I recommend the article for indexing in presented form.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?YesCompeting Interests: No competing interests were disclosed.
Table 3 contains a list of relevant software tool versions and sources.

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.
https://doi.org/10.21956/wellcomeopenres.22142.r86974