The genome sequence of a beetle-killing wasp, Tiphia femorata (Fabricius, 1775)

We present a genome assembly from an individual female Tiphia femorata (a beetle-killing wasp; Arthropoda; Insecta; Hymenoptera; Tiphilidae). The genome sequence is 276 megabases in span. Most of the assembly (98.73%) is scaffolded into 12 chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 22.4 kilobases in length. Annotation of the genome in Ensembl identified 10,470 protein-coding genes.


Background
Tiphia femorata (Fabricius, 1775), a beetle-killing wasp, is an abundant species in most of Europe, the eastern Palaearctic and North Africa (Museum für Naturkunde, no date; Peeters, 2004).In Great Britain, it mainly inhabits warmer, dry and semi-arid grasslands and meadows, and has been recorded from Cornwall to Kent, south Wales and north to Norfolk, and has also been sighted in the Channel Islands (Archer, 2001).T. femorata is a univoltine species and can be encountered from June through September, feeding on nectar and pollen of flowers (especially on Apiaceae species).
Tiphia femorata is a small wasp: lengths range from 5 to 12 mm in males and from 6 to 15 mm in females.The body is entirely black, except for the rear two pairs of legs, which are reddish brown (Museum für Naturkunde, no date).
Tiphia femorata is the most common species of Tiphiidae.Like most members of Tiphiidae, it is a parasitoid.The larvae of T. femorata prey on the Scarabaeidae Rhizotrogus solstitialis and Anisoplia austriaca and several Aphodius species (Aphodiidae) (Bogusch, 2007).The female burrows into the soil to find the beetle larval host, stinging the victim to temporarily paralyse it, then laying an egg in the cuticle of the host.The T. femorata larva hatches and feed externally on the beetle grub.
The genome of T. femorata 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 T. femorata, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a single female T. femorata specimen (Figure 1) collected in Wytham Great Wood.A total of 75-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 11 missing joins or misjoins and removed 1 haplotypic duplication, reducing the assembly size by 0.18% and the scaffold number by 5.66%, and increasing the scaffold N50 by 6.04%.
The final assembly has a total length of 276 Mb in 50 sequence scaffolds with a scaffold N50 of 25.8 Mb (Table 1).Most (98.73%) of the assembly sequence was assigned to 12 chromosomal-level scaffolds, representing 12 autosomes (numbered by sequence length) (Figure 2-Figure 5; Table 2).The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 96.0% (single 95.7%, duplicated 0.3%) using the OrthoDB v10 hymenoptera reference set (n = 5,991).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A single female T. femorata specimen (iyTipFemo1) was collected on 13 August 2019 in Wytham Great Wood, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.773, longitude -1.333).The specimen was netted by Liam Crowley (University of Oxford), who also identified the species.The specimen was then snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute.The iyTipFemo1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Whole organism 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 between 12-20 kb in a Megaruptor 3 system with a speed setting of 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

Raw data accessions
PacificBiosciences SEQUEL II ERR9467445 Hi-C Illumina ERR9435037 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 sequencing libraries were constructed according to the manufacturers' instructions.Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on a Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were generated in the Tree of Life laboratory from the remaining whole organism tissue of iyTipFemo1 using the Arima v2 kit and sequenced on a HiSeq 10X instrument.

Genome assembly
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., 2022).The assembly was checked for contamination   environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the T. femorata assembly (GCA_944319695.1).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Ethics/compliance issues
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   The authors presented the genome assembly of Tiphia femorata, a beetle-killing wasp whose larvae prey on various beetle larvae.They found 10,470 protein-coding genes.They also assembled the complete mitochondrial genome.This paper is worth publishing.I have just a few minor suggestions.
Tiphia femorata, the wasp sequenced here, probably represents a species complex (see FaunaEuropea -https://fauna-eu.org/).Could the authors clarify the identification issue?Also, the common host Rhizotrogus solstitialis is a synonym of Amphimallon solstitiale, so A. solstitiale is the correct species name.Please correct.

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: diversity and ecology of parasitoid wasps 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.

Feng Zhang
Nanjing Agricultural University, Nanjing, China The authors present a genome assembly from an individual female Tiphia femorata by combining HiFi long reads and HI-C data.This chromosomal-level assembly spans approximately 276 Mb with 98.73% of the assembly being scaffolded into 12 chromosomal pseudomolecules.
As a result, it produces a high-quality genome assembly.Furthermore, gene annotation performed on this assembly using Ensembl has identified 10,470 protein-coding genes.
In the Genome sequence report, the authors mentioned that the deposited assembly represents one haplotype.However, they also indicated that contigs corresponding to the second haplotype have been deposited.While the accession of the alternate haplotype is provided, it would be beneficial to include specific assembly information, such as the genome size and scaffold N50.
Minor revisions: In Background, change "is an abundant species in most of Europe" to "is an abundant species in most areas of Europe".

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: Insect genomics, phylogenomics 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.Image of the Tiphia femorata specimen taken prior to preservation and processing.

Figure 2 .
Figure 2. Genome assembly of Tiphia femorata, iyTipFemo1.1: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 276,162,441 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 (38,663,132 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (25,801,794 and 16,818,620 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 at the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/iyTipFemo1.1/dataset/CALUEP01/snail.

Figure 5 .
Figure 5. Genome assembly of Tiphia femorata, iyTipFemo1.1:Hi-C contact map.Hi-C contact map of the iyTipFemo1.1 assembly, visualised in HiGlass.Chromosomes are arranged in size order from left to right and top to bottom.The interactive Hi-C map can be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=eT742vyJSUO1PVEDGgOgZg.

Table 3 . Software tools used. Software tool Version Source
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