The genome sequence of a chalcid wasp, Gastracanthus pulcherrimus (Westwood, 1833)

We present a genome assembly from an individual female Gastracanthus pulcherrimus (a chalcid wasp; Arthropoda; Insecta; Hymenoptera; Pteromalidae). The genome sequence is 1,010.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.4 kilobases in length.


Background
With females measuring around 5 mm in length, Gastracanthus pulcherrimus is a relatively large species of the chalcid wasp family Pteromalidae.It is also a striking species, slender, with a particularly long pronotum, metallic green hues and, in females, two large dark patches on each fore wing.Like most parasitoid wasps, G. pulcherrimus is poorly known but it is fairly easily found in deciduous woodland and has a wide range across Europe (Noyes, 2019), recorded from the Republic of Ireland, Northern Ireland (Thuróczy & O'Connor, 2009) and from England, but not yet from Wales or Scotland (Dale-Skey et al., 2016).
Despite its relative conspicuousness, knowledge about the biology of G. pulcherrimus is not extensive.It belongs to the subfamily Trigonoderinae, which all seem to be parasitoids of Coleoptera (Graham, 1969).Gastracanthus pulcherrimus is associated with wood and has been reported as a parasitoid of a Sphenoptera species (Coloptera: Buprestidae (Ghahari & Huang, 2012).Graham (1969) expresses doubt about a supposed rearing from an adult byrrhid beetle.By analogy with related Pteromalidae, G. pulcherrimus is presumably an idiobiont ectoparasitoid, i.e., hosts will be permanently paralysed, and the larva develops externally on the host.
The family Pteromalidae, for a long time an unwieldy assemblage of disparate chalcid lineages, has recently been split into many different, hopefully monophyletic families (Burks et al., 2022).Gastracanthus is among ten genera comprising the subfamily Trigonoderinae, itself one of eight subfamilies within the diverse and species rich Pteromalidae family.All previously published genomes belong to species in the subfamily Pteromalinae (Martinson et al., 2017;Werren et al., 2010).

Genome sequence report
The genome was sequenced from one female Gastracanthus pulcherrimus (Figure 1) collected from Wytham Woods, UK (51.77,.A total of 27-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 48 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 6.49%, and increasing the scaffold N50 by 0.45%. The final assembly has a total length of 1,010.0Mb in 143 sequence scaffolds with a scaffold N50 of 186.8 Mb (Table 1).
Most (95,67%) of the assembly sequence was assigned to 5 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/2922068.

Sample acquisition and nucleic acid extraction
Two adult Gastracanthus pulcherrimus were collected from Bert's Pheasant Pen, Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.31) on 2021-09-02, using a light trap.The collectors were Gavin Broad, Chris Fletcher and Inez Januszczak (Natural History Museum).The specimens were identified by Gavin Broad and then dry-frozen at -80°C.The specimen used for DNA sequencing was specimen ID NHMUK014451697, ToLID iyGasPulc2, while specimen ID NHMUK014451655, ToLID iyGasPulc1 was used for Hi-C scaffolding.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyGasPulc2 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Tissue from the whole organism 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 1.8X 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 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 IIe (HiFi) instrument.Hi-C data were also generated from whole organism tissue of iyGasPulc1 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) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).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 using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format     et al., 2020) andBUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.
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 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

Daniel Garcia-Souto
Bioquímica, xenética e inmunoloxía, Universidade de Vigo (Ringgold ID: 16784), Vigo, Galicia, Spain This manuscript presents a chromosome-level genome assembly of Gastracanthus pulcherrimus, a species of chalcid wasp in the family Pteromalidae.The study provides significant insights into the genomic structure of this relatively understudied species, with a genome span of 1,010.0megabases.The assembly was primarily scaffolded into five chromosomal pseudomolecules, covering 95.67% of the genome, which highlights the high degree of completeness in the assembly.The authors also sequenced and assembled the mitochondrial genome, which is 24.4 kilobases in length, potentially indicating expansions or repeats in the control region that would, in my honest opinion, require some validation.
The manuscript makes a notable contribution to the genomic data of the genus, as this is one of the few genomes from the Pteromalidae family outside the Pteromalinae subfamily.Although the final assembly's BUSCO score is slightly lower than the desired threshold (92.6% completeness), this is still a strong result for a genome of such complexity.

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.
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.Reviewer Expertise: population genetics, genomics 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 Gastracanthus pulcherrimus, iyGasPulc2.1: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 1,010,024,266 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 (222,508,353 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (186,761,157 and 179,352,141 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/iyGasPulc2.1/dataset/CASCKD01/snail.

Figure 5 .
Figure 5. Genome assembly of Gastracanthus pulcherrimus, iyGasPulc2.1:Hi-C contact map of the iyGasPulc2.1 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=Yrs3ERn6RL-maDBtEFqvcA.
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.

Reviewer Report 04
September 2024 https://doi.org/10.21956/wellcomeopenres.21890.r95766© 2024 Koch J.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.Jonathan Berenguer Uhuad KochUSDA-ARS Pollinating Insect Research Unit, Maryland, USAThe article describes a genome assembly of Gastracanthus pulcherrimus from a female specimen.The authors clearly articulate the generation of the genome assembly using PacBio HiFi and HiC.The genome assembly still needs to be annotated, and in currently in the queue.One minor pointRephrase "The family Pteromalidae, for a long time an unwieldy assemblage of disparate chalcid lineages, has recently been split into many different, hopefully monophyletic families" to "The family Pteromalidae, for a long time an unwieldy assemblage of disparate chalcid lineages, has recently been split into many different, likely monophyletic families"○ Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.