The genome sequence of a parasitoid wasp, Ichneumon xanthorius Forster, 1771

We present a genome assembly from an individual female Ichneumon xanthorius (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein coding genes.


Background
Ichneumon xanthorius is an idiobiont endoparasitoid of Lepidoptera, ovipositing in the host pupa, arresting its development, consuming it entirely and pupating within the host pupal shell. It has been reared from pupae of several species of Noctua Linnaeus and Xestia Hübner (Lepidoptera: Noctuidae) in experiments where females were presented with potential hosts (Hinz & Horstmann, 2007); although the natural host range is poorly known, it will be limited to noctuid moths with larvae which feed low in the vegetation and pupate in the spring. This is a univoltine species, with females active post-hibernation mainly in April and May and then the next generation from July to September, sometimes into October, before spending the winter in concealed locations, such as under bark. Males are seen from mid-June to late August, mostly in July (data from iRecord; requires registration) and do not over-winter. The species is widely distributed across Europe, North Africa, the Middle East and into Central Asia. In Britain, I. xanthorius seems to be most frequent in southern England but has also been widely recorded in Scotland, Wales and Ireland (Broad, 2016;O'Connor et al. 2007; data from iRecord). Found mainly in open areas, including gardens, and often seen on flowers, especially umbels.
In common with many species of the subfamily Ichneumoninae, Ichneumon xanthorius is strongly sexually dimorphic, although both females and males have distinctive colour patterns which mean the species is unlikely to be confused with any other in Northern Europe. Females have a yellow-and black-striped metasoma (abdomen minus the first segment, which is fused with the thorax in apocritan Hymenoptera), males have the metasoma extensively yellow anteriorly with a characteristic large yellow spot on the hind coxa too.
To our knowledge, this is the first chromosomal genome produced for an ichneumonid wasp. The Ichneumonidae, or Darwin Wasps, comprise one of the great radiations of metazoan life, with over 25,000 described (and many more undescribed) species attacking a huge variety of (mostly) holometabolous insects (Broad et al., 2018;Klopfstein et al., 2019). Genomic data will help us uncover some of the adaptations that have enabled this success.

Genome sequence report
The genome was sequenced from a single female I. xanthorius ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.770, longitude -1.331). A total of 55-fold coverage in Pacific Biosciences single-molecule long reads and 62-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 85 missing/misjoins and removed 1 haplotypic duplication, reducing the assembly size by 0.05% and scaffold number by 32.13%, and increasing the scaffold N50 by 57.52%.
The final assembly has a total length of 315 Mb in 150 sequence scaffolds with a scaffold N50 of 20.1 Mb (Table 1). Of the assembly sequence, 82.64% was assigned to 12 chromosomal-level scaffolds (numbered by sequence length) (Figure 2- Figure 5; Table 2). The orientation of chromosome 10, region 1.08-1.74 Mb cannot be determined from available data. The assembly has a BUSCO v5.1.2 (Manni et al., 2021) completeness of  95.5% (single 95.2%, duplicated 0.4%) using the hymenop-tera_odb10 reference set (n=5991). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Genome annotation report
The iyIchXant1.1 genome has been annotated using the Ensembl rapid annotation pipeline (   using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 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 between 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 sequencing libraries were constructed according to the manufacturers' instructions. Sequencing was performed by the Scientific Operations core at the Wellcome Sanger   Institute on Pacific Biosciences SEQUEL II and Illumina NovaSeq 6000 instruments. Hi-C data were generated from head tissue using the Arima v2.0 kit and sequenced on an Illumina NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021). Haplotypic duplication was identified and removed with purge_ dups (Guan et al., 2020). Scaffolding with Hi-C data (Rao et al., 2014) was carried out with SALSA2 (Ghurye et al.,  2019). The Hi-C scaffolded assembly was polished with the 10X Genomics Illumina data by aligning to the assembly with longranger align, calling variants with freebayes (Garrison & Marth, 2012). One round of the Illumina polishing was applied. The mitochondrial genome was assembled with MitoHiFi (Uliano- Silva et al., 2021), which performed annotation using MitoFinder (Allio et al., 2020). The assembly was checked for contamination as described previously (Howe et al., 2021). Manual curation (Howe et al., 2021) was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext. The genome was analysed within the BlobToolKit environment (Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Ichneumon xanthorius assembly (GCA_917499995.1). Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein to-genome alignments of a select set of proteins from UniProt (PMID: 30395287).

Reviewer Expertise: Insect genomics, endogenous viruses
One briefly mentioned characteristic of the wasp that is of comparative interest is that it is an idiobiont endoparasitoid of host pupae. As an endoparasitoid, it is likely to have some strategy for evading the immune system of its host insect. Most genomic studies of endoparasitoids have been of koinobiont species that attack host larvae, and with associations with symbiotic viruses that are involved with these immunological interactions. It would thus be of interest whether this ichneumonid also possesses a similar virus, or whether it has some other battery of genes for host immune evasion. There are some known (published) core viral gene sequences from the viruses that are housed within other ichneumonid wasps (Campopleginae, Banchinae) that could be used as probes (although it is possible of course that if this wasp species does carry a virus, it might be too distantly related to the other viruses to recognize).

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.
Parasitoid wasp genomics, venom 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.