The genome sequence of a digger wasp, Ectemnius continuus (Fabricius, 1804)

We present a genome assembly from an individual female Ectemnius continuus (digger wasp; Arthropoda; Insecta; Hymenoptera; Crabronidae). The genome sequence is 260.3 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 9,835 protein coding genes.


Background
Ectemnius continuus is a small to medium sized digger wasp in the family Crabronidae.It is widespread throughout the Holarctic, and in the UK it is a common species, particularly across the south.It is black with yellow markings on the scapes, pronotum, tibiae and tergites.It is one of two British species of Ectemnius with reduced yellow marking on tergites 1 and 3, and is larger and more common than the other species with this pattern, E. rubicola.The clypeus is covered with shining silver hairs.Unusually for aculeates, the male Ectemnius do not have an additional antennal segment, with both sexes possessing 12 segments.Male E. continuus have unique small spines on the first and second tarsomeres of the mid tarsus.
It occurs in a wide range of habitats including woodlands, gardens and farmland.It is univoltine, with a flight period from early May to late September, however, it is likely to be bivoltine in the south of the UK.Females hunt medium-sized Diptera such as syrphids, muscids and calliphorids (Archer, 1995).Tabanidae and Therevidae have also been recorded prey (Lomholdt, 1975).Nests are constructed in cavities in dead wood, such as old beetle burrows in tree stumps and standing dead wood.Nest structure varies from straight to branching, and may contain up to 10 cells, with each cell provisioned with six to eight flies (Lomholdt, 1975).Adults are strongly associated with the flowers of umbellifers, including angelica, hogweed, wild carrot, wild parsnip, fennel, cow parsley and water-dropwort, which they visit for both nectar and prey.
The complete genome sequence for this species will facilitate studies into the evolution of hunting strategies, reproductive systems and Hymenopteran taxonomy.

Genome sequence report
The genome was sequenced from one female Ectemnius continuus (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 92-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 132-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 43 missing joins or mis-joins and removed 9 haplotypic duplications, reducing the assembly length by 2.65% and the scaffold number by 10.1%, and increasing the scaffold N50 by 23.41%. The final assembly has a total length of 260.3 Mb in 347 sequence scaffolds with a scaffold N50 of 15.4 Mb (Table 1).
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.Most (92.21%) of the assembly sequence was assigned to 14 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 diploid female.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/1126389.

Sample acquisition and nucleic acid extraction
A female Ectemnius continuus (specimen ID Ox000186, ToLID iyEctCont1) was netted in Wytham Woods, Oxfordshire (biological vice-county Berkshire), 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 iyEctCont1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Head and thorax 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.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.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)  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 Ectemnius continuus assembly (GCA_910591665.1).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.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material • Legality of collection, transfer and use (national and international)

Rodolpho S.T. Menezes
State University of Santa Cruz, Ilhéus, Brazil The manuscript by Crowley presents a genome assembly from a female of the digger wasp, Ectemnius continuus (Fabricius, 1804).The final assembly is 260.3 megabases and most of the assembly is scaffolded into 14 chromosomal pseudomolecules.
Overall the manuscript presents an advance in the genomic field of wasps.This genome information will be interesting for comparative genomics investigation 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, with attention for the mitochondrial genome.The assembled mitogenome was 27.05 kilobases in length, it is unusual for wasps in general.
Minor point: 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?Partly 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, however I have significant reservations, as outlined above.

Miles Zhang
The University of Edinburgh, Edinburgh, Scotland, UK The authors report the chromosome scale assembly of the genome sequence of the crabronid wasp, Ectemnius continuus, obtained using state-of-the-art methodologies.The background provides important information on the life history of the species including interactions with its hosts.
Similar to other genome notes from this group, the genome sequence is of very high quality and will be a valuable source for comparative genetics, evolutionary biology, and phylogenomic studies.
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: Phylogenomics, systematics, evolutionary ecology 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.
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: Comparative genomics, genome assembly, population genetics, multiple species (Plants, Hymenoptera, Birds) 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 Ectemnius continuus, iyEctCont1.1: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 260,364,363 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 (26,542,703 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (15,408,693 and 9,697,251 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/iyEctCont1.1/dataset/CAJUYD01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Ectemnius continuus, iyEctCont1.1:Hi-C contact map of the iyEctCont1.1 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=ZKIZReSkS1arzsdQMBNaig.

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.
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.