The genome sequence of the Wasp Spider, Argiope bruennichi (Scopoli, 1772)

We present a genome assembly from an individual female Argiope bruennichi (the Wasp Spider; Arthropoda; Arachnida; Araneae; Araneidae). The genome sequence is 1,778.4 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.06 kilobases in length.


Background
The Wasp Spider Argiope bruennichi (Scopoli, 1772) is a large and distinctive species of Araneid (orb-weaving) spider.The vernacular name refers to the black and yellow banding across the female's abdomen which resembles the patterning of a social wasp.Several hypotheses have been suggested for the function of the female's colouration, with Bush et al. (2008) concluding that it most likely evolved as a means of attracting insect prey to the spiders' webs, as opposed to being a form of camouflage (by breaking up the spider's outline).The same authors state that the possibility of aposematism playing a role in the evolution of the banding requires further study.Adult males are much smaller than adult females and lack the bold markings of the latter, instead having a pale brown abdomen with two vague, lighter longitudinal stripes.
Another intriguing characteristic of A. bruennichi (and other Argiope spp., which do not occur in the UK) is the zigzag stabilimentum, a pattern of thick silk which extends down from the centre of their webs.Like the spider's pattern, this has led to many theories about its purpose.It was originally considered to have a stabilising function, although this view has been largely dismissed due to the loose attachment to the web (Starks, 2002).The stabilimentum is formed from the same type of silk as the spider uses for wrapping up prey, and Walter et al. (2008) suggest it functions as a mechanism to maintain high silk gland activity, allowing more efficient 'wrap attack'.
Argiope bruennichi was first recorded in the UK at Rye Harbour in 1922 and until the 1970s was very localised along the south coast of England, but has spread north and west rapidly since then (Bee et al., 2020).While most British records are still confined to the south-east, there are many records from Cornwall and it has now been recorded as far north as East Yorkshire (British Arachnological Society, 2023).The species is characteristic of unmanaged grassland, wasteland and verges, spinning large orb webs in low vegetation.Orthoptera are the main prey, although a range of insects are taken.Adults peak in August and large, distinctive, urn-shaped egg-sacs are positioned higher in the vegetation with eggs overwintering (Bee et al., 2020).
The species has been extensively studied, with many papers published on various aspects of its biology and ecology.This is not the first publication dealing with its genomics: for example, Sheffer et al. (2021) published a chromosome-level reference genome for the species, and its complete mitochondrial genome (Zhang et al., 2016) and sex chromosomes (Sheffer et al., 2022) have also been sequenced.
We present a chromosomally complete genome sequence for Argiope bruennichi, using the standardised procedures set by the Darwin Tree of Life programme, ensuring consistency and comparability with other genomes sequenced within this project.

Genome sequence report
The genome was sequenced from one female Argiope bruennichi (Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (51.77,.A total of 28-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 10 missing joins or mis-joins and removed 5 haplotypic duplications, reducing the assembly length by 0.25% and the scaffold number by 21.05%, and increasing the scaffold N50 by 2.39%. The final assembly has a total length of 1,778.4Mb in 29 sequence scaffolds with a scaffold N50 of 139.1 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 (99.93%) of the assembly sequence was assigned to 13 chromosomal-level scaffolds, representing 11 autosomes and the X 1 and X 2 sex chromosomes.The X 1 and X 2 chromosomes were determined based on alignment to a published assembly of Argiope bruennichi (GCA_ 015342795.1)(Sheffer et al., 2021).The sex chromosomes were identified in the published genome based on read mapping and cytology (Sheffer et al., 2022).Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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.
The RNA concentration was 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 the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus 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) and Illumina
NovaSeq 6000 (RNA-Seq) instruments.Hi-C data were also generated from remaining cephalothorax tissue of qqArgBrue1 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 as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, 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.
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 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)

Jesper Bechsgaard
Section for Genetic Ecology and Evolution, Department of Biology, Aarhus University, Aarhus, Denmark The Data Note presents the genome sequencing of the spider species, Argiope bruennichi.Cutting edge technologies have been used to generate data and bioinformatic processing seem proper.RNA has been sequenced, but has not been used for the annotation of protein coding genes, which I find should have been done.

Zhi-Sheng Zhang
School of Life Sciences, Southwest University, Chongqing, Chongqing, China This manuscript presents a genome assembly from an individual female Argiope bruennichi .The genome sequence is 1,778.4megabases in span, and the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X1 and X2 sex chromosomes.The mitochondrial genome has also been assembled.One more thing needs improvement: In Figure 5, the chromosome ID should be marked.

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 spiders from South China; Systematics, Phylogeny and biogeography of several spider groups, such as Lycosidae, Agelenidae, Dictynidae, Hahniidae, Amaurobiidae, Titanoecidae, etc.; Adapation of some spiders in different habitats; Spider silk.
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.
bruennichi, with most of the 1.7 Gb assembly length anchored into 13 chromosome-scale scaffolds, including the two sex chromosomes X1 and X2, and a BUSCO completeness of 98.1% complete BUSCOs.The assembly is an improvement over the previously published assembly (Sheffield et al., 2021).
The rationale for generating this new assembly is not clearly stated.Yes, it is in improved assembly, but the report does not mention this.The only reason given is the consistency with the other Tree of Life genome assemblies.However, for me, this is not reason enough to generate a new assembly, as thousands of genomes of equally good quality are generated by other projects across the globe.I would have liked to see a comparison to the previously published assembly and a brief statement or discussion of what the new genome can provide to the scientific community that the other one did not already.
In addition, the methods are not sufficiently described for my liking.I am not a fan of publications that do not state the parameters used to generate the data but instead redirect the reader to a list of other publications or protocols to be reproducible.Especially as the bioinformatics protocols are somewhat hidden or unclear.

Is the rationale for creating the dataset(s) clearly described? No
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Partly
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: genome assembly, sequencing, population 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, however I have significant reservations, as outlined above.

Figure 2 .
Figure 2. Genome assembly of Argiope bruennichi, qqArgBrue1.1: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 1,778,398,216 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 (151,336,912 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (139,055,214 and 127,865,338 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 arachnida_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Argiope%20bruennichi/dataset/CANOBD01/snail.

Figure 3 .
Figure 3. Genome assembly of Argiope bruennichi, qqArgBrue1.1: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/Argiope%20bruennichi/dataset/CANOBD01/blob.

Figure 4 .
Figure 4. Genome assembly of Argiope bruennichi, qqArgBrue1.1: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/Argiope%20bruennichi/dataset/CANOBD01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Argiope bruennichi, qqArgBrue1.1:Hi-C contact map of the qqArgBrue1.1 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=e6_6dMh-TI-b_f7lmn0Zjg.

Is the rationale for creating the dataset(s) clearly described? Partly Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Partly Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
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.