The genome sequence of an ichneumonid wasp, Amblyteles armatorius (Forster, 1771)

We present a genome assembly from an individual male Amblyteles armatorius (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 216 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.6 kilobases in length.


Background
Amblyteles armatorius (Forster, 1771) is a large (12-16 mm) and slender species of wasp from the family Ichneumonidae.It is the only species in its genus found in Britain (Broad, 2016).It can be distinguished by the details of the yellow stripes on the black metasoma (abdomen beyond the first segment) and propodeum (first abdominal segment, fused to the thorax) with a pair of lateral spines.As with many species of the subfamily Ichneumoninae the sexes are strongly dimorphic, but each is distinctive.The female has an amblypygous ovipositor (short, almost concealed by the hypopygium) adapted to ovipositing in lepidopteran larvae.The larvae of A. armatorius are internal parasitoids of Xestia and Noctua species (Lepidoptera, Noctuidae) (Broad et al., 2018), emerging from the pupae.
Amblyteles armatorius is very common, with a wide but scattered distribution across Britain and Ireland.The adults can be found flying from May to July and October to November (Prehn & Raper, 2016), with only females on the wing latterly.They can often be seen flying low among the vegetation.Adult wasps feed on sugar-rich sources such as nectar and honeydew; they are particularly common on umbellifers (Broad et al., 2018;Leius, 1960;Martin, 1986).Hinz (1985) described the biology of this species, by breeding A. armatorius in captivity using caterpillars of its principal host, the Large Yellow Underwing moth, Noctua pronuba (Linnaeus, 1758).A single male and a female of A. armatorius hatched from moth puparia on 31 May and 14 June respectively and copulated on 15 June.The female was fed water and honey.It ceased feeding on 01 August.Over a month later (16 September) it was removed from the jar and offered young larvae of N. pronuba.It oviposited in three of them, after which the female wasp was euthanised and dissected.It contained 10 to 12 eggs on each side, with 1 to 2 mature eggs (Hinz, 1985).
The caterpillars are parasitised in the autumn.The ichneumon larva feeds inside the caterpillar, over-wintering inside the host's pupa.The adults emerge in late spring and copulate soon after (Hinz, 1985).Males are relatively short-lived.Fertilised females have been found aestivating, as do Noctua pronuba, and hibernate, which is more usual for European Ichneumoninae.Favoured diapause sites are caves and buildings in Belgium and Netherlands, with one case of an aggregation of twenty individuals reported in September from a church crypt (Verheyde & Quicke, 2022).A large group of females was also observed at altitude on Vogelberg mountain (Switzerland) running excitedly on a tall log stack, presumably in search of aestivation sites (Hinz, 1985).Amblyteles armatorius has been reported to be infected by the fungus Ophiocordyceps ditmarii in Europe (Mornand et al., 2012).
The high-quality genome of A. armatorius was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for A. armatorius, based on one male specimen from Luton.

Genome sequence report
The genome was sequenced from one male A. armatorius (Figure 1) collected from Luton, UK (51.88, -0.37).A total of 66-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 12 missing joins or mis-joins, reducing the scaffold number by 9.09%.
The final assembly has a total length of 215.8 Mb in 40 sequence scaffolds with a scaffold N50 of 18.9 Mb (Table 1).Most (95.39%) of the assembly sequence was assigned to 12 chromosomal-level scaffolds, which were all autosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 93.4% (single 93.2%, duplicated 0.3%) using the hymenoptera_odb10reference set.

Sample acquisition and nucleic acid extraction
Two male Amblyteles armatorius specimens (iyAmbArma2; NHMUK014111036 and iyAmbArma4; NHMUK014111055) were swept using an insect net from vegetation in Wigmore Park, Percival Way, Wigmore, Luton, England (latitude 51.88, longitude -0.37).The specimen yAmbArma2; NHMUK014111036 was swept on 2 June 2020 and iyAmbArma4; NHMUK014111055 on 16 June 2020.They were collected by Olga Sivell and identified by Gavin Broad (both Natural History Museum,    London) and then snap-frozen on dry ice.The tissue samples taken from the two specimens were stored in a CoolRack prior to sample preparation and genome sequencing.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyAmbArma2 sample was weighed and dissected on dry ice.Thorax tissue 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.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 1.8× 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.
RNA was extracted from thorax tissue of iyAmbArma4 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.DNA and RNA sequencing were performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi), Illumina HiSeq 4000 (RNA-Seq) and HiSeq X Ten (10X) instruments.Hi-C data were also generated from head tissue of iyAmbArma2 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Ethics/compliance issues
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The The authors sequenced and assembled the parasitic wasp genome of Amblyteles armatorius (Forster, 1771).The introduction provides valuable information on various aspects of the biology of this parasitic species, including data on the host of noctuid caterpillars.I only suggest adding a sentence about the possible importance of known hosts in forestry and agriculture.

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: Entomology 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.Amblyteles armatorius (Forster, 1771): a) A live specimen (NHMUK014111036) placed in a plastic tube upon collection.b) Image of the specimen taken during preservation and processing.

Figure 2 .
Figure 2. Genome assembly of Amblyteles armatorius, iyAmbArma2.1: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 215,787,317 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 (24,262,552 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,898,530 and 11,422,841 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/iyAmbArma2.1/dataset/CAKOFT01/snail.

Figure 5 .
Figure 5. Genome assembly of Amblyteles armatorius, iyAmbArma2.1:Hi-C contact map.Hi-C contact map of the iyAmbArma2.1 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=ZWLIofWNSi6-MiniR9_Waw.

Table 3 . Software tools and versions used. Software tool Version Source
Darwin Tree of Life Partner is subject to the Darwin Tree of Life Project Sampling Code of Practice.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.Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.