The genome sequence of an ichneumonid wasp, Exephanes ischioxanthus (Gravenhorst, 1829)

We present a genome assembly from an individual male Exephanes ischioxanthus (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 284.0 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.43 kilobases in length.


Background
Exephanes ischioxanthus is an ichneumonid, or 'Darwin wasp', widely distributed and frequently common in grassy areas.It is found across much of Europe (Yu et al., 2016), with adults on the wing in summer, particularly June and July.As with many species of the subfamily Ichneumoninae, females are mainly black but with the metasoma (abdomen beyond the first segment) red medially and with white spots on the antennae, scutellum and the posterior of the metasoma.However, the ovipositor projects further than in most Ichneumoninae and the end of the metasoma is a little elongated, with eight metasomal tergites clearly visible.Males look very different, with the metasoma yellow centrally and the face entirely yellow.Specimens can be easily identified using Perkins (1960), but Hinz and Horstmann (2000) offer a more reliable identification key to the European Exephanes, with information on ecology.
The distinctive metasoma and ovipositor of Exephanes species are adaptations towards oviposition into larvae of noctuid moth larvae in grass stems and E. ischioxanthus is a parasitoid of Mesoligia furuncula (Denis & Schiffermüller), the Cloaked Minor (Hinz & Horstmann, 2000).Oviposition is into the larva and emergence, as in almost all Ichneumoninae, is from the host pupa (Broad et al., 2018).Both sexes can be found feeding on flowers and the sequenced individual was a male found on an umbel.Females have been found swarming over low vegetation in warm, humid weather just before storms (G.Broad, pers.obs.).

Genome sequence report
The genome was sequenced from one male Exephanes ischioxanthus (Figure 1) collected from Oare Marshes, England, UK (51.34, 0.89).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 110 missing joins or mis-joins, reducing the scaffold number by 37.5%, and increasing the scaffold N50 by 22.81%.
The final assembly has a total length of 284.0 Mb in 84 sequence scaffolds with a scaffold N50 of 23.9 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 (98.8%) of the assembly sequence was assigned to 12 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).The specimen is a haploid male.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 male Exephanes ischioxanthus (specimen ID NHMUK010636399, ToLID iyExeIsch1) was collected from Oare Marshes, England UK (latitude 51.34, longitude 0.89) on 2021-06-20 using an aerial net.The specimen was collected and identified by Gavin Broad (Natural History Museum) and preserved by dry freezing at -80 °C.
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 iyExeIsch1 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 head and 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.

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 instrument.Hi-C data were also generated from remaining head and thorax tissue of iyExeIsch1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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 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     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 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

Rahia Mashoodh
University College London, London, England, UK This is a detailed genome for the parasitic wasp Exephanes ischioxanthus.Given the sheer number of wasp species in this family, it would be nice to have a sentence or two explaining the broader interest of the species to the community.For example, for understanding genome dynamics, evolution, or ecological differences between different communities or species of this parasitic wasp.
Is the rationale for creating the dataset(s) clearly described?

Sarah Inwood
University of Otago, Dunedin, Otago, New Zealand The authors sequenced and assembled a chromosomal scale genome assembly for the parasitic wasp genome of Exephanes ischioxanthus (Gravenhorst, 1829) using HiFi and Hi-C data.This has generated a high-quality genome assembly, using technically sound assembly and QC methods, and is well-written.

Minor comments:
The significance of having a genome available for E. ischioxanthus is not made immediately clear to readers.

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The methods describing what tissues were used for each sequencing method (HiFi and Hi-C) could be clearer, with the head reported to be used by both methods.

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The method for mitochondrial genome assembly could also be clarified, as the authors mention using MitoHiFi which can use MitoFinder or MITOS but do not report which one was used for their assembly.

Brendan Pinto
Arizona State University, Tempe, AZ, USA The authors describe the high-quality genome assembly of the Ichneumon wasp, Exephanes ischioxanthus.The manuscript is technically sound and uses assembly and QC pipelines that have been previously vetted through use (and reuse) by the Sanger Institute.Reference genomes are certainly important to have for investigating myriad interesting scientific questions, however, the importance of this specific genome is not made entirely clear (at least to me) for a broader readership.Regardless, the note is well-written, describes an important resource for genomics in an interesting clade of hymenopterans.
Is the rationale for creating the dataset(s) clearly described?Partly 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: My expertise is in genomics of squamate reptiles.I was also involved in the group who published one of the first chromosome-level genomes for a braconid wasp (genus Cotesia).
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 Exephanes ischioxanthus, iyExeIsch1.1: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 284,017,360 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 (30,499,120 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (23,927,040 and 17,743,748 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/Exephanes%20ischioxanthus/dataset/iyExeIsch1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Exephanes ischioxanthus, iyExeIsch1.1:Hi-C contact map of the iyExeIsch1.1 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=GVHDG0BnSbWn8WvXMQdKVw.

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

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.
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.

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 Competing Interests:
No competing interests were disclosed. ○Is

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.
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.