The genome sequence of the Saxon Wasp, Dolichovespula saxonica (Fabricius, 1793)

We present a genome assembly from an individual male Dolichovespula saxonica (the Saxon Wasp; Arthropoda; Insecta; Hymenoptera; Vespidae). The genome sequence is 221.8 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,856 protein coding genes.


Background
The Saxon Wasp, Dolichovespula saxonica, is medium-sized (11-18 mm) social wasp in the family Vespidae.It occurs across the Palaearctic from northern and central Europe to northern Asia and Japan (Archer, 1999).It was first recorded from the UK in Surrey in 1987 (Allen & Archer, 1989) and has since spread throughout Britain, reaching northwards to Scotland.It is now common and widespread across the UK.D. saxonica is very similar in appearance to D. norwegica, to which it is closely related.It lacks the pair of red markings on the second gastral tergite which D. norwegica often has, and the hairs on the side of the thorax are light brown rather than black.
It can be found across a range of open habitats, including heathland, open woodland and urban environments.It is a eusocial species, forming colonies of up to around 1,800 individuals (Nadolski, 2012).Overwintered queens emerge and initiate nests around May. Paper nests are typically constructed in aerial situations such as trees and shrubs 2 to 7 m above the ground, although a range of other sites are known including buildings, tree holes and beehives (Archer, 2006).Workers are produced from early June and males and new queens from early July.Mature nests contain an average of approximately 1300 cells across three to five combs (Archer, 2006).As with other species in the genus, D. saxonica exhibits low effective paternity and relatively high incidence of worker reproduction (Foster et al., 2001).D. saxonica is a generalist predator, taking a wide variety of prey.It feeds on nectar from a wide range of flowers.Queens are known to visit bilberry flowers in the spring and workers and males are recorded visiting wild angelica, wild parsnip and hogweed.It is able to lay pheromone trails used for foraging and orientation (Steinmetz & Schmolz, 2003).
The complete genome sequence for this species, along with recent publication of Vespinae genomes, including Dolichovespula (Falk et al., 2022), Vespa (Crowley et al., 2022), and Vespula (Crowley et al., 2021), will facilitate studies into many areas such as the evolution of sociality, reproductive systems and Hymenopteran taxonomy.

Genome sequence report
The genome was sequenced from one male Dolichovespula saxonica (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 27-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 115-fold coverage in 10X Genomics read clouds were generated.
Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 288 missing joins or mis-joins, reducing the scaffold number by 55.2%, and increasing the scaffold N50 by 137.4%.
The final assembly has a total length of 221.8 Mb in 112 sequence scaffolds with a scaffold N50 of 9.5 Mb (Table 1).Most (92.54%) of the assembly sequence was assigned to 26 chromosomal-level scaffolds.A summary of the assembly statistics is shown in Figure 2, 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.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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/85443.

Sample acquisition and nucleic acid extraction
A male Dolichovespula saxonica (specimen ID Ox000189, ToLID iyDolSaxo1) was netted in Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.33) on 2019-08-20.The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyDolSaxo1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Head and thorax tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.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.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 was 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 abdomen tissue of iyDolSaxo1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
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.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Dolichovespula saxonica assembly (GCA_911387935.1).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).

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.

Rodolpho Menezes
Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Brazil The manuscript by Liam Crowley presents a genome assembly from a male of the saxon wasp, Dolichovespula saxonica.The final assembly is 221.8Mb in 112 sequence scaffolds.Overall the manuscript presents an advance in the genomic field of social wasps.This genome information will be interesting for comparative genomics investigation within Vespidae and also for evolution and conservation studies.The methodology is thorough and explained and the figures are well constructed and the manuscript is well written.However, I think the author should compare its results with the assembled genomes from other wasp species.Moreover, since the author assembled the mitochondrial genome, I think it is interesting to show general (GC/AT content…) mitochondrial information about this species." 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.

Lucio Navarro-Escalante
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA

Overall:
The manuscript describes the sequencing, assembly and annotation of the genome of the wasp Dolichovespula saxonica.This work shows a high quality chromosome-level assembly obtained by combining PacBio HiFi reads, 10X Illumina PE reads and Hi-C scaffolding from a single male individual.The full sequence of its mitochondrial genome is also reported.The manuscript is well written, clear and includes all the necessary methodological details.All raw data is publicly available as well.Tables and figures are well explanatory and relevant.This genome assembly report seems to be an important contribution for improving biological understanding of members within the Vespidae wasp family.Despite one minor comment, I support the indexing of this report and its data.

Minor comment:
In the "Genome sequence report" section, authors should include that the number of chromosome-level scaffolds obtained agrees with previous karyotype analysis by Hoshiba et al. (1989).

Reference:
Hoshiba H, Matsuura M, Imai HT: Karyotype Evolution in the Social Wasps Hymenoptera, Vespidae.This is a data note reporting the assembly of the nuclear and mitochondrial genomes of the wasp Dolichovespula saxonica available at NCBI since July 2021.One single male was used for multiple sequencing strategies (genome sequencing, Hi-C, and transcriptomic data).The methods used for the assembly were the default pipeline of the DToL project, which is well accepted and known to result in good quality and complete genome assemblies.As the current reported assembly.
I have no major comments about this report, only a few minor suggestions that do not reduce the overall quality of the manuscript: -On Table 1 the assembly release date has one extra 0 that should be deleted (from 20201-07-21 to 2021-07-21) -In the "Genome annotation report" section there is only information about the annotation of the nuclear genome.What were the results of the mtcontig annotation?-In the Methods, section "Genome assembly, curation and evaluation" it says "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)...", which one (MitoFinder or MITOS) was used to annotate the mtcontig of D. saxonica?
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 Dolichovespula saxonica, iyDolSaxo1.1: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 221,852,803 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 (23,378,875 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (9,507,211 and 3,928,253 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/Dolichovespula%20saxonica/dataset/CAJVQX01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Dolichovespula saxonica, iyDolSaxo1.1:Hi-C contact map of the iyDolSaxo1.1 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=EP4az_NHSS-9fl8YSI6n0Q.

Reviewer Report 16
February 2024 https://doi.org/10.21956/wellcomeopenres.22343.r72987© 2024 Navarro-Escalante L. 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.

Table 3 . Software tools: versions and sources. Software tool Version Open 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.

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 Natalia Araujo
Unit of Evolutionary Biology & Ecology -, Universite Libre de Bruxelles, Brussels, Brussels, Belgium