The genome sequence of a false flower beetle, Anaspis maculata (Geoffroy in Fourcroy, 1785)

We present a genome assembly from an individual female Anaspis maculata (false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The genome sequence is 757.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,965 protein coding genes.


Background
Anaspis maculata (Geoffroy in Fourcroy, 1785) is a small saproxylic beetle in the Scraptiidae family, also known as false flower beetles.Members of the genus Anaspis are diurnal and readily fly when disturbed, usually occurring amongst flowers in the of Rosaceae and Apiaceae families where they have been recorded to mate and feed, though they have also been found in tree foliage (Duff & Schmidt, 2020;Levey, 2009).Anaspis larvae are recorded to feed on fungi and wood fibres but are also considered general scavengers, they can be found beneath loose bark and emerge as adults from May to August (Duff & Schmidt, 2020;Levey, 2009).
Anaspis maculata has a variety of colour forms, the most common of which consists of yellow colouration to the base of the antennae, upper side and legs, with dark brown marks on the elytra: triangular on the scutellum and oval at the middle of the elytra.This species measures 2.4-3.1 mm in length (Levey, 2009).
A. maculata is widespread and abundant throughout the UK, with few records in northern Scotland and some records from Ireland.It can be found through western Europe from Denmark then south to Portugal and, from Germany, eastwards to Italy (NBN Atlas Partnership, 2023; UK Beetles, no date).
Being widespread throughout its range has made A. maculata a useful indicator species in studies investigating saproxylic beetle species and the health of forests (Foster et al., 2019;Lachat et al., 2012).The full genome for this species will help assist these studies and improve our understanding of how widespread saproxylic beetles can impact and are impacted by changing forest health.
The genome of Anaspis maculata 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 Anaspis maculata, based on one specimen collected from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from one female Anaspis maculata (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 30-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 27 missing joins or mis-joins and removed 6 haplotypic duplications, reducing the assembly length by 0.15%, and the scaffold N50 by 0.42%. The final assembly has a total length of 757.8 Mb in 49 sequence scaffolds with a scaffold N50 of 95.7 Mb (Table 1).The snail plot 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 (99.34%) of the assembly sequence was assigned to 8 chromosomal-level scaffolds, representing 7 autosomes and the X sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).The X chromosome was assigned based on synteny with Lagria hirta (GCA_947359425.1).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
The specimen used for genome sequencing was a female Anaspis maculata (specimen ID Ox001433, ToLID icA-naMacu3), collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2021-05-25 by beating.The specimen was collected and identified by Mark Telfer (independent researcher) and preserved by snap-freezing on dry ice.
The specimen used for Hi-C sequencing (specimen ID NHMUK014400216, ToLID icAnaMacu2) was hand-picked on Imperial Wharf, Fulham, UK (latitude 51.47, longitude -0.18).The specimen was collected and identified by Maxwell Barclay (Natural History Museum) and preserved by dry freezing at -80°C.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the icAnaMacu3 sample was weighed and dissected on dry ice (Jay et al., 2023).Tissue from the whole organism was homogenised using  Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument.Hi-C data were generated from the whole organism tissue of icAnaMacu2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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,   et al., 2021;Simão et al., 2015) were calculated.

Genome assembly, curation and evaluation
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Anaspis maculata assembly (GCA_949128115.1) in Ensembl Rapid Release.

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.
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) DSL2 pipelines "sanger-tol/readmapping" (Surana et al., 2023a) and "sanger-tol/genomenote" (Surana et al., 2023b).The 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

Phillip Davidson
Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA In their genome report, Telfer et al., present a complete and high quality reference assembly for the false flower beetle Anaspis maculata.The rationale, methodology, and data availability are sound and appropriate for the study.I have a handful of revision suggestions that I think will clarify the results of this data set, as listed below.

○
In methods and results, please specify what developmental stage the specimen used for sequencing was (adult, pupa, larva).

José María Martín-Durán
Queen Mary University of London, London, UK This genome note reports the assembly and annotation of the genome of the beetle Anaspis maculata.This is a common species in the UK and most parts of Western Europe.This genome will help investigate the diversity of Coleoptera and contribute to ecological and evolutionary studies.
Strengths of the resource: High quality assembly, annotated following the high standards of the Darwin Tree of Life.

Doga Cedden
Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, Göttingen, Germany Data note by Telfer et al. presents a high-quality genome assembly from Anaspis maculata.The background information about this saproxylic beetle is adequately covered in the data note.The method is sufficiently described and appropriate, and the authors also present a sufficient quality assessment of the assembly.Below are several comments for consideration: False flower beetle may refer to Scraptiidae or sometimes specifically to the genus Anaspis but not specifically to Anaspis maculata.This is appropriately indicated in the title by "a false flower beetle."Could the authors also indicate this in the abstract?Rather than "false flower beetle," it could be referred to as "a member of a false flower beetle" or "a false flower beetle" in parentheses. 1.
It would have been better to provide some kind of scale in Figure 1, which is commonly done in other submissions by the Darwin Tree of Life Project.Please consider this in future submissions.

2.
Could the authors check the GC% provided in Table 2? I found it a bit surprising that all autosomal chromosomes had a "40.0%"GC content.It could also be the actual values, which is totally fine.

3.
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: I work on coleopteran pests using RNA interference and RNA-seq.

Figure 2 .
Figure 2. Genome assembly of Anaspis maculata, icAnaMacu3.1:metrics.The BlobToolKit snail plot 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 757,844,310 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 (141,817,626 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (95,735,550 and 62,968,389 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/icAnaMacu3_1/dataset/icAnaMacu3_1/snail.

Figure 3 .
Figure 3. Genome assembly of Anaspis maculata, icAnaMacu3.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icAnaMacu3_1/dataset/icAnaMacu3_1/blob.

Figure 4 .
Figure 4. Genome assembly of Anaspis maculata, icAnaMacu3.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icAnaMacu3_1/dataset/icAnaMacu3_1/cumulative.
Assembly was carried out withHifiasm (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.The assembly was checked for contamination and corrected as described previously(Howe et al., 2021).Manual curation was performed using HiGlass(Kerpedjiev et al., 2018)  andPretext (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.

Figure 5 .
Figure 5. Genome assembly of Anaspis maculata, icAnaMacu3.1:Hi-C contact map of the icAnaMacu3.1 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=Syc7nGBCQiuwB-jdPHSPDA.

○
Methods and approaches are well described.○ 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: Evolutionary biology, comparative 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.Reviewer Report 09 July 2024 https://doi.org/10.21956/wellcomeopenres.23539.r88825© 2024 Cedden D. 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.

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.

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:
Figure2, BUSCO miniplot: The percentages displayed add up to greater than 100%, suggesting an error in the labelling.The middle shade of green I think represents single copy, not complete, composition.Please check and if this true, an accurate plot and labelled should be supplied.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, however I have significant reservations, as outlined above.
© 2024 Martín-Durán J.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.