The genome sequence of an ichneumonid wasp, Heteropelma amictum (Fabricius, 1775)

We present a genome assembly from an individual female Heteropelma amictum (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 226.4 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.65 kilobases in length.


Background
Heteropelma amictum is one of our more conspicuous ichneumonid wasps in late summer and autumn, often seen in rather slow flight over bushes and shrubs with its clear yellow extremities nearly glowing.The red metasoma (the apparent abdomen) and yellow hind tarsi and antennae contrast strongly with the black mesosoma (thorax plus the first abdominal segment).Various species of the subfamily Anomaloninae share a very similar body shape and basic colour pattern but most (in Europe at least) are smaller and lack the particularly bright end to the antenna.The wing venation of Heteropelma species is relatively distinctive (see Gauld, 1976;Gauld & Mitchell, 1977).Males of H. amictum are seen more frequently, presumably searching for females, and at close range can be recognised by the strongly widened second hind tarsal segment.Identification of H. amictum is relatively straightforward using Gauld and Mitchell (1977) or Pénigot (2021), with the latter being more reliable for the subfamily Anomaloninae as a whole.The species has a very wide range, from most of Britain across Europe and Asia to Indonesia (Gauld, 1976).
Found in various habitats, but particularly more open areas with shrubs, H. amictum has been reared from a variety of mediumsized caterpillars of the families Erebidae and Noctuidae (Gauld & Mitchell, 1977).As with other Anomaloninae, the female oviposits in the host when it is a larva, with the wasp larva completing its development in the host pupa.All anomalonines of known biology are solitary parasitoids and the long legs and petiolate metasoma seem to be used to jab the caterpillar with the ovipositor from a distance, with the metasoma swung beneath the wasp's body.How anomalonine larvae survive within the bodies of a range of host species is unknown, but there are reports that the larvae of at least some species might be protected within a trophamnion, a layer of cells surrounding the early instar larvae (Rosenberg, 1934;Tothill, 1922).This is the first published genome for a species of Anomaloninae, and the growing body of genomes for the clade of ophioniform ichneumonid wasps should help us understand some of the innovations which have enabled this massive radiation of endoparasitoid koinobiont parasitioid wasps, i.e., wasps with larvae which develop within the active larvae of their hosts.

Genome sequence report
The genome was sequenced from one female Heteropelma amictum (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.76,.A total of 101-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 142 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 75.36%, and increasing the scaffold N50 by 83.43%. The final assembly has a total length of 226.4 Mb in 16 sequence scaffolds with a scaffold N50 of 29.3 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 (99.95%) of the assembly sequence was assigned to 10 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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 Heteropelma amictum (specimen ID Ox000709, ToLID iyHetAmic1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude -1.33) on 2020-07-30.The specimen was collected by Liam Crowley (University of Oxford) and identified by Gavin Broad (NHM) and preserved on dry ice.
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 iyHetAmic1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing (as per the protocol at https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1).For sample homogenisation, the abdomen tissue of the iyHetAmic1 sample was homogenised    et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
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 values were calculated in Merqury (Rhie et al., 2020).This work    Table 3 contains a list of relevant software tool versions and sources.

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 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

Jerome Hui
The Chinese University of Hong Kong, Hong Kong, Hong Kong Crowley and colleagues report the genome sequence of wasp Heteropelma amictum (Fabricius 1775).This species can be found in many places in Britain.Molecular data of this species are mainly confined to COI and ribosomal sequences (as well as transcriptomes) deposited to the NCBI database.This new genome resource is important and will be very useful for further studies, such as understanding the ecological, evolutionary, and genomics questions related to insects more widely.
This genome resource is excellent from the summary statistics, with good BUSCO numbers, high sequence continuity (scaffold N50), and majority of sequences contained on the 10 pseudochromosomes (plus mitochondrion).To sum up, this is another valuable contribution from the Darwin Tree of Life Consortium.

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: Genomics, evolution, invertebrates 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.Crowley and Broad present a data note on the chromosome level genome assembly of Heteroplema amictum.As for many other of DToL's data notes, the underlying raw data is sufficient and of high quality, methods are described in a way to ensure reproducibility and results are very good.
In general, there are only a few minor remarks.
In the first sentence of the Background paragraph, you write "is one of our more".Despite being written from a British perspective, I would recommend rephrasing "our" to something more general (e.g."one of Britain's most" or simply "one of the most"). 1.
Not sure if this will be fixed during production but Figure 2 has low resolution and looks not ideal.

2.
In the contact map (Figure 5) there is one region in the middle of the third largest scaffold, which shows signal to all regions in the assembly (red cross).Do you know what caused this?Is this a technical artifact? 3.

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?

Figure 2 .
Figure 2. Genome assembly of Heteropelma amictum, iyHetAmic1.1: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 226,445,852 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 (39,331,219 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,282,975 and 13,633,056 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/Heteropelma%20amictum/dataset/iyHetAmic1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Heteropelma amictum, iyHetAmic1.1:Hi-C contact map of the iyHetAmic1.1 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=Kez2u_yFTGaghwgCqkxGEQ.

Reviewer Report 07
February 2024 https://doi.org/10.21956/wellcomeopenres.22550.r72009© 2024 Schell T. 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.Tilman Schell 1 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany 2 Senckenberg Research Institute, Frankfurt am Main, Germany Review of The genome sequence of an ichneumonid wasp, Heteropelma amictum (Fabricius, 1775) from L. M. Crowley and G. R. Broad

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Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).

Peer Review Current Peer Review Status: Version 1
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.