
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

10.12688/wellcomeopenres.20498.1
Data Note
Articles
The genome sequence of an ichneumonid wasp, Exephanes ischioxanthus (Gravenhorst, 1829)
[version 1; peer review: 2 approved, 1 approved with reservations]

Broad Gavin R. Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0001-7223-5333
1
Natural History Museum Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Natural History Museum, London, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

8 1 2024
2024
9 816 11 2023
Copyright: © 2024 Broad GR et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.

Exephanes ischioxanthus
an ichneumonid wasp
genome sequence
chromosomal
Hymenoptera
Wellcome Trust218328 Wellcome Trust206194 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Ichneumonoidea; Ichneumonidae; Ichneumoninae; Ichneumonini; Exephanes; Exephanes ischioxanthus (Gravenhorst, 1829) (NCBI:txid2884240).

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%.

Figure 1. Photograph of the Exephanes ischioxanthus (iyExeIsch1) specimen used for genome sequencing.

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.

Table 1. Genome data for Exephanes ischioxanthus, iyExeIsch1.1.

Project accession data	
Assembly identifier	iyExeIsch1.1	
Species	Exephanes ischioxanthus	
Specimen	iyExeIsch1	
NCBI taxonomy ID	2884240	
BioProject	PRJEB58956	
BioSample ID	SAMEA110019319	
Isolate information	iyExeIsch1, male: head and thorax (DNA sequencing and Hi-C
data)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	59.4	≥ 50	
k-mer completeness	100%	≥ 95%	
BUSCO **	C:95.0%[S:94.7%,D:0.3%],F:1.5%,M:
3.5%,n:5,991	C ≥ 95%	
Percentage of assembly
mapped to chromosomes	98.8%	≥ 95%	
Sex chromosomes	-	localised homologous pairs	
Organelles	Mitochondrial genome assembled	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10798428	
Hi-C Illumina	ERR10786029	
Genome assembly	
Assembly accession	GCA_958510785.1	
Span (Mb)	284.0	
Number of contigs	544	
Contig N50 length (Mb)	1.1	
Number of scaffolds	84	
Scaffold N50 length (Mb)	23.9	
Longest scaffold (Mb)	30.5	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).

** BUSCO scores based on the hymenoptera_odb10 BUSCO set using v5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Exephanes%20ischioxanthus/dataset/iyExeIsch1_1/busco.

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 3. Genome assembly of Exephanes ischioxanthus, iyExeIsch1.1: BlobToolKit GC-coverage plot.

Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Exephanes%20ischioxanthus/dataset/iyExeIsch1_1/blob.

Figure 4. Genome assembly of Exephanes ischioxanthus, iyExeIsch1.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Exephanes%20ischioxanthus/dataset/iyExeIsch1_1/cumulative.

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 2. Chromosomal pseudomolecules in the genome assembly of Exephanes ischioxanthus, iyExeIsch1.

INSDC
accession	Chromosome	Length (Mb)	GC%	
OY294015.1	1	30.5	43.0	
OY294016.1	2	28.8	43.0	
OY294017.1	3	28.35	43.0	
OY294018.1	4	27.48	42.0	
OY294019.1	5	26.8	42.5	
OY294020.1	6	23.93	42.5	
OY294021.1	7	22.62	42.0	
OY294022.1	8	20.37	42.5	
OY294023.1	9	18.95	42.5	
OY294024.1	10	18.21	42.0	
OY294025.1	11	17.74	42.5	
OY294026.1	12	16.9	40.5	
OY294027.1	MT	0.02	14.5	

The estimated Quality Value (QV) of the final assembly is 59.4 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 95.0% (single = 94.7%, duplicated = 0.3%), using the hymenoptera_odb10 reference set ( n = 5,991).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/2884240.

Methods

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.

Protocols developed in the Tree of Life laboratory are publicly available on protocols.io: https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v1.

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.

Genome assembly, curation and evaluation

Assembly was carried out with Hifiasm ( Cheng et al., 2021). The assembly was then scaffolded with Hi-C data ( Rao 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 MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt 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 was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

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

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.1.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
sanger-tol/genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/
readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
YaHS	1.2a	https://github.com/c-zhou/yahs	

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

•   Legality of collection, transfer and use (national and international)

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.

Data availability

European Nucleotide Archive: Exephanes ischioxanthus. Accession number PRJEB58956; https://identifiers.org/ena.embl/PRJEB58956 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Exephanes ischioxanthus 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 Table 1.

Author information

Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7139035.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.22691.r91542
Reviewer response for version 1
Mashoodh Rahia 1Referee https://orcid.org/0000-0003-3065-9044

1 University College London, London, England, UK
3 9 2024 Copyright: © 2024 Mashoodh R
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
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.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

behaviour, genomics, evolution, sociality

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.

10.21956/wellcomeopenres.22691.r74030
Reviewer response for version 1
Inwood Sarah 1Referee https://orcid.org/0000-0001-6661-293X

1 University of Otago, Dunedin, Otago, New Zealand
28 8 2024 Copyright: © 2024 Inwood S
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove-with-reservations
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.

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.

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.

Are sufficient details of methods and materials provided to allow replication by others?

Partly

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genomics, host-parasite interactions, parasitoid wasps, insects, viruses, biocontrol

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, however I have significant reservations, as outlined above.

10.21956/wellcomeopenres.22691.r74032
Reviewer response for version 1
Pinto Brendan 1Referee https://orcid.org/0000-0002-4243-5788

1 Arizona State University, Tempe, AZ, USA
27 2 2024 Copyright: © 2024 Pinto B
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
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.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Partly

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
==== Refs
Abdennur N Mirny LA : Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36 (1 ):311–316. 10.1093/bioinformatics/btz540 31290943
Allio R Schomaker-Bastos A Romiguier J : MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20 (4 ):892–905. 10.1111/1755-0998.13160 32243090
Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69 (2 ):313–319. 10.1016/j.ympev.2012.08.023 22982435
Broad GR Shaw MR Fitton MG : The ichneumonid wasps of Britain and Ireland (Hymenoptera: Ichneumonidae): Their classification and biology.In: Handbooks for the Identification of British Insects.Telford: Royal Entomological Society and Field Studies Council,2018;7 . 10.1079/9781800625471.0000
Challis R Richards E Rajan J : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10 (4 ):1361–1374. 10.1534/g3.119.400908 32071071
Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18 (2 ):170–175. 10.1038/s41592-020-01056-5 33526886
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
Harry E : PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps. 2022; [Accessed 19 October 2022]. Reference Source
Hinz R Horstmann K : Die westpaläarktischen Arten von Exephanes. Wesmael (Insecta, Hymenoptera, Ichneumonidae, Ichneumoninae). Spixiana. 2000;23 :15–32. Reference Source
Howe K Chow W Collins J : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10 (1 ): giaa153. 10.1093/gigascience/giaa153 33420778
Kerpedjiev P Abdennur N Lekschas F : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19 (1 ): 125. 10.1186/s13059-018-1486-1 30143029
Manni M Berkeley MR Seppey M : BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38 (10 ):4647–4654. 10.1093/molbev/msab199 34320186
Perkins JF : Hymenoptera: Ichneumonoidea; Ichneumonidae, Subfamilies Ichneumoninae II, Alomyinae, Agriotypinae and Lycorininae. Handbooks for the Identification of British Insects. 1960;7 (2(aii) ):117–213. Reference Source
Rao SSP Huntley MH Durand NC : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159 (7 ):1665–1680. 10.1016/j.cell.2014.11.021 25497547
Rhie A McCarthy SA Fedrigo O : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592 (7856 ):737–746. 10.1038/s41586-021-03451-0 33911273
Rhie A Walenz BP Koren S : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21 (1 ): 245. 10.1186/s13059-020-02134-9 32928274
Simão FA Waterhouse RM Ioannidis P : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31 (19 ):3210–3212. 10.1093/bioinformatics/btv351 26059717
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a; [Accessed 21 July 2023]. 10.5281/zenodo.7755665
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b; [Accessed 21 July 2023]. 10.5281/zenodo.6785935
Uliano-Silva M Ferreira JGRN Krasheninnikova K : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023;24 (1 ): 288. 10.1186/s12859-023-05385-y 37464285
Vasimuddin M Misra S Li H : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).IEEE,2019;314–324. 10.1109/IPDPS.2019.00041
Wellcome Sanger Institute: The genome sequence of an ichneumonid wasp, Exephanes ischioxanthus (Gravenhorst, 1829). European Nucleotide Archive.[dataset], accession number PRJEB58956,2023.
Yu DS van Achterberg C Horstmann K : Taxapad 2016, Ichneumonoidea 2015. Database on flash-drive.Ontario, Canada: Nepean,2016.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
