The genome sequence of an ichneumonid wasp, Tromatobia lineatoria (Villers, 1789)

We present a genome assembly from an individual female Tromatobia lineatoria (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 383.6 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 23.25 kilobases in length.


Background
Tromatobia lineatoria is an attractively marked ichneumonid wasp ('Darwin wasp') of the subfamily Pimplinae, usually richly patterned with red and cream against a black background.Unlike some similar Tromatobia species, the conspicuous yellow orbital stripe is acutely angled near the hind ocellus.Across much of Europe and the Near East, T. lineatoria is the most frequently encountered Tromatobia species, often found around houses, as its larvae feed on spider egg sacs, including those of common garden species such as Zygiella x-notata (Clerck) and Araneus diadematus Clerck.Probably occurring throughout Britain and Ireland, T. lineatoria adults can be found from spring to late autumn and are at least double brooded (Fitton et al., 1988).Note that in the older literature, this species was usually named Tromatobia oculatoria, which was an old misidentification (Horstmann, 2001).
Although belonging to a family of parasitoid wasps, Tromatobia species are essentially predators.Eggs are laid within the silken egg sacs of spiders, with known hosts mainly Araneidae but also Linyphiidae, Philodromidae and Tetragnathidae.The larvae of T. lineatoria are usually gregarious, with brood sizes of one to six, each larva consuming spider eggs in succession.Any spider guarding the egg sac is not attacked and if any spider eggs remain, spiderlings can emerge (Fitton et al., 1988;Nielsen, 1923).Larvae from late autumn broods will feed slowly through the winter, with adults emerging in the spring (Fitton et al., 1987).
Within the subfamily Pimplinae there is a wide range of host associations and developmental biology.Townes (1969) proposed that the remarkable polysphinctines, larvae of which develop on active spiders, arose from parasitoids of silk-cocooned moths, via an intermediate life history of attacking silken egg sacs.This evolutionary pathway has been supported by phylogenetic studies (Gauld et al., 2002;Matsumoto, 2016;Spasojevic et al., 2021), and Tromatobia occupies an intriguing phylogenetic position either as part of a radiation of spider egg sac predators (Gauld et al., 2002;Matsumoto, 2016) or as the closest relatives of Gregopimpla, which are gregarious parasitoids of cocooned moth pupae.Either way, the genome of T. lineatoria, together with genomes of polysphinctines and other related pimplines (e.g., Broad et al., 2023), should help us understand some of the adaptations which enabled these transitions.

Genome sequence report
The genome was sequenced from one female Tromatobia lineatoria (Figure 1) collected from Pulborough, UK (50.96, -0.51).A total of 58-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 45 missing joins or misjoins and removed one haplotypic duplication, reducing the scaffold number 16.25%, and increasing the scaffold N50 by 7.59%.
The final assembly has a total length of 383.6 Mb in 66 sequence scaffolds with a scaffold N50 of 19.0 Mb (Table 1).Most (98.1%) of the assembly sequence was assigned to 21 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).The order and orientation of contigs on SUPER_7 between 17Mb and 21 Mb is uncertain.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/2776060.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.

Sample acquisition and nucleic acid extraction
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 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 (HiFi) instrument.Hi-C data were also generated from remaining head/thorax tissue of iyTroLine1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Software tool Version
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

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Systematics, evolution 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.

Zoltán Vas
Hungarian Natural History Museum, Budapest, Hungary I am glad to see that more and more genome sequence of ichneumon wasps species are published.These, including the present study, are important footsteps to untangle and understand the evolutionary history of this hyperdiverse family.I agree with the arguments of the authors why the phylogenetic position of Tromatobia lineatoria is important, so why this species is indeed a good candidate for genome sequencing.
Being a morphology-based, traditional taxonomist, I am not completely up to date about the used molecular methodology, so it is partly beyond my abilities to evaluate.Though, the same lab has published sevaral similar, highly regarded papers, so I feel safe to say that everything is fine here.

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: traditional, morphology-based taxonomy of Ichneumonidae 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 Tromatobia lineatoria, iyTroLine1.1: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 383,602,644 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 (27,496,960 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (19,039,001 and 12,934,278 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/iyTroLine1.1/dataset/CATIWW01/snail.

Figure 5 .
Figure 5. Genome assembly of Tromatobia lineatoria, iyTroLine1.1:Hi-C contact map of the iyTroLine1.1 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=cZepPc8bQ0qO5ZccVO9iEQ.

Reviewer
Report 26 July 2024 https://doi.org/10.21956/wellcomeopenres.21962.r88838© 2024 Vas Z.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.

Table 3
Wellcome Sanger Institute -Legal and GovernanceThe 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 ' contains a list of relevant software tool versions and sources.

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

Table 2 . Chromosomal pseudomolecules in the genome assembly of Tromatobia lineatoria, iyTroLine1. INSDC accession Chromosome Length (Mb) GC%
Wellcome Sanger Institute, 2023).The genome sequence is released openly for reuse.The Tromatobia lineatoria genome sequencing initiative is part of the Darwin Tree of Life (DToL) project.All raw sequence data and the assembly have been deposited in INSDC databases.The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute.Raw data and assembly accession identifiers are reported in Table1.