The genome sequence of the Black Spongefly, Sisyra nigra (Retzius, 1783)

We present a genome assembly from an individual female Sisyra nigra (the Black Spongefly; Arthropoda; Insecta; Neuroptera; Sisyridae). The genome sequence is 372.6 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length.


Background
Sisyra nigra, the Black Spongefly, or Spongillafly in North America, is a fascinating lacewing.The larvae eat freshwater sponges of the genera Ephydatia and Spongilla in lakes, ponds and slow-moving rivers (Plant, 1997), apparently with little host specificity towards the sponges (Poirrier, 1969).The female spongefly lays eggs on branches overhanging the water and the larvae are fully aquatic, at first free-swimming and then feeding within the sponge tissue, with many morphological and physiological adaptations to their unique niche (Jandausch et al., 2019).Pupation is on land.Adults disperse from water bodies and on overcast, humid nights can be light-trapped some distance from waterbodies, as was the case with these specimens collected for sequencing.Adults of Sisyra nigra are basically black, with an infuscate wing membrane, are small (about 5 mm long) and rest in a typical lacewing fashion, with the wings held in a tent-like shape over the body.They are mostly carnivorous, feeding on mites, insect eggs and sometimes aphids, as well as honeydew (Devetak & Klokočovnik, 2016).
A Holarctic species (Bowles, 2006), Sisyra nigra is one of only three British species of the family Sisyridae, all in the genus Sisyra, and is by the far the most widely distributed within Britain (NBN Atlas Partnership, 2023;Plant, 1997).The combination of the entirely dark antennae and fore wings distinguishes S. nigra from the other two British species (Plant, 1997).This is the first genome for a species of Sisyridae and as such will help towards piecing together the evolution and radiation of the Neuroptera, an ancient insect order with diverse life histories.

Genome sequence report
The genome was sequenced from one female Sisyra nigra (Figure 1) collected from Kent, Tonbridge, Kent, UK (51.19, 0.29).A total of 55-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 117 missing joins or mis-joins and removed 49 haplotypic duplications, reducing the assembly length by 2.16% and the scaffold number by 31.71%, and increasing the scaffold N50 by 0.43%.
The final assembly has a total length of 372.6 Mb in 111 sequence scaffolds with a scaffold N50 of 50.8 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, 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 (95.76%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds, representing 6 autosomes and the X sex chromosome.The X chromosome was identified based on reduced Hi-C signal (PacBio from female, Hi-C appears to be from male).An inversion between 20 Mb and 22 Mb on Chromosome 1 likely corresponds to difference between samples used for PacBio and Hi-C.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.

Sample acquisition and nucleic acid extraction
A female Sisyra nigra (specimen ID NHMUK010634999, ToLID inSisNigr1) was collected in a light trap in Tonbridge, Kent, UK (latitude 51.19, longitude 0.29) on 2020-06-24.The specimen was collected and identified by Gavin Broad (Natural History Museum) and kept in DESS for 2 weeks before being frozen at -80°C.

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers'   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 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

Are the protocols appropriate and is the work technically sound? No
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: Systematic Entomology 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. Reviewer

Importance and Contribution
The genome sequencing of Sisyra nigra marks the first complete genome assembly for a species of the family Sisyridae, making a significant contribution to the field of genomics and entomology.This study offers valuable insights into the Neuroptera order's genetic makeup and evolutionary history.The detailed assembly provides a robust foundation for future comparative genomics and biological research, particularly in understanding the unique adaptations of the Black Spongefly to its aquatic environment.
The availability of this genome sequence opens new avenues for studying the genetic basis of the Black Spongefly's ecological interactions, developmental biology, and evolutionary adaptations.Moreover, the high-quality data and methodologies presented can serve as a reference for genomic studies in other related species, enhancing our overall understanding of insect genomics.The study's meticulous approach to data acquisition and genome assembly sets a benchmark for future projects, ensuring reproducibility and accuracy.
Overall, this work not only enriches our knowledge of Sisyra nigra but also contributes significantly to the broader scientific understanding of insect biodiversity and evolution.
## Questions 1. Mitogenome Details: The abstract mentions the mitochondrial genome assembly but needs more detail.Can you provide more information about the completeness and characteristics of the mitogenome in the main text?
2. Distribution Clarification: The paper mentions that Sisyra nigra is found in the Holarctic region and North America.Can you clarify whether it is found in both areas or specify any distinctions in its distribution?
3. Chromosome Data: The article states that most of the genome is scaffolded into seven chromosomal pseudomolecules, including the X chromosome.Are there any unique characteristics or findings related to the X chromosome that should be highlighted?
4. Genome Completeness: The paper mentions a BUSCO completeness score of 97.1%.Can you explain how this score compares to other insect genome assemblies?
5. Gene Annotations: Are any noteworthy genes or gene families identified in this assembly related to the spongefly's unique ecological adaptations?
## Suggestions 1. Abstract Enhancement: Enhance the abstract by including specific results and their implications, such as unique findings about the genome structure or any significant annotations.
2. Methodology Details: While the methods are well-documented, consider adding a brief overview of each critical process in the main text to improve readability and provide context before diving into detailed protocols.: Ensure all figures (e.g., Hi-C contact maps, GC-coverage plots) have clear, descriptive legends.This helps readers understand the data at a glance.

Figures and Tables
4. Data Availability: In the "Data availability" section, it might be helpful to include direct links to crucial datasets and resources to facilitate access for other researchers.

Xiumei Lu
1 Shanghai Academy of Agricultural Sciences, Shanghai, China 2 University of Bristol, Bristol, England, UK The experiment combined sophisticated methodologies to ensure a reliable and high-quality assembly of the Sisyra nigra genome.It represents the first whole genome assembly of Sisyra nigra , offering valuable data for potential biological investigations and comparative genomics analyses.
In the abstract, the authors mentioned that the mitogenome was also assembled.So, it is necessary to explicitly state more about the mitogenome, indicating whether it is complete or not.
The authors introduced the significance of this spongefly species and emphasized the outstanding aquatic adaptation of Sisyridae.However, the authors should recheck the distribution of Sisyra nigra, as there seems to be some confusion regarding whether it is distributed in North America, the Holarctic region, or elsewhere.
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: My research areas are systematics, paleobiology and phylogenomics of the superorder Neuropterida (Insecta: Holometabola) to provide critical evidence for the understanding of its evolutionary history.
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 Sisyra nigra, inSisNigr1.1: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 372,608,688 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 (64,276,211 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (50,790,609 and 31,345,168 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 endopterygota_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Sisyra%20nigra/dataset/inSisNigr1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Sisyra nigra, inSisNigr1.1: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/Sisyra%20nigra/dataset/inSisNigr1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Sisyra nigra, inSisNigr1.1: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/Sisyra%20nigra/dataset/inSisNigr1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Sisyra nigra, inSisNigr1.1:Hi-C contact map of the inSisNigr1.1 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=EWZtAmYIS12BnjH_wfvHGg.
Report 25 May 2024 https://doi.org/10.21956/wellcomeopenres.22477.r84398© 2024 Cosme 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.Luciano Cosme Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA Review of Scientific Article on the Genome Sequence of the Black Spongefly, Sisyra nigra The article "The genome sequence of the Black Spongefly, Sisyra nigra (Retzius, 1783)" presents a comprehensive genome assembly of an individual female Black Spongefly.This study, led by Gavin R. Broad and his team, reports a genome sequence spanning 372.6 megabases, scaffolded into seven chromosomal pseudomolecules, including the X sex chromosome.To ensure high coverage and accuracy, the researchers utilized advanced sequencing techniques such as Pacific Biosciences single-molecule HiFi long reads and Hi-C data.The assembled mitochondrial genome is 16.34 kilobases in length.The final assembly demonstrates high quality, with a Quality Value (QV) of 60.3 and a BUSCO completeness score of 97.1%.

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
5. Comparative Analysis: Include a section or paragraph comparing the Sisyra nigra genome to those of closely related species or other Neuropterida, discussing evolutionary implications or unique genomic features.
Competing Interests: No competing interests were disclosed.Reviewer Expertise: Genomics, population genetics, GWAS 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.
Reviewer Report 15 December 2023 https://doi.org/10.21956/wellcomeopenres.22477.r69903© 2023 Lu X.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.