The genome sequence of the Judas Tree Seed Beetle, Bruchidius siliquastri Delobel, 2007

We present a genome assembly from an individual male Bruchidius siliquastri (the Judas tree Seed Beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 375.6 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,940 protein coding genes.


Background
Bruchidius siliquastri was described as new to science based on specimens collected in southern France by Delobel in Kergoat et al. (2007), who also cite specimens from Hungary and China (not included in the type series).They assume that the species was imported to Europe from China.It has since been reported from Slovakia (Kollár et al., 2009), Belgium (Hanssens, 2009), the Czech Republic (Šefrova et al., 2010), Bulgaria (Stojanova et al., 2011), Serbia (Gavrilović & Savić, 2013), Germany (Rheinheimer & Hassler, 2013), Turkey (Hizal & Parlak, 2013), Ukraine (Martynov & Nikulina, 2015), Italy (Yus Ramos & Bocci, 2017), Romania (Pintilioaie et al., 2018), Korea (Jeong et al., 2022), as well as from Spain, where its life history and immature stages have been explored (Yus Ramos et al., 2009a;Yus Ramos et al., 2009b;Yus Ramos et al., 2009c).It was first reported in Britain from South Kensington in 2014 (Barclay, 2014) and has since become widespread in the London area and in other cities and towns in southern Britain.Although Britain is the northern limit of its currently known distribution, the beetle is actively expanding its range, and trees where it was apparently absent 5 to 10 years ago now support populations.
B. siliquastri develops in the seed pods of leguminous trees of the genus Cercis (Fabaceae), particularly the Judas tree Cercis siliquastrum Linnaeus.Cercis occurs throughout the northern hemisphere, and while the Judas tree is native to southern Europe and western Asia, it is a popular planted ornamental in cities and parks elsewhere because of its bright flowers and attractive foliage.It is common in the Levant, and may owe its name to a legend that Judas Iscariot hanged himself from one (Barclay, 2014), but the majority of London specimens are much too small for this.An alternative theory is that the name is a corruption of 'Judea', the apparent origin of European specimens.The tree features in Middle Eastern art and poetry, and the edible flowers and young leaves are sometimes used as a culinary garnish, but there is no indication that the beetle was present in Europe or Western Asia until the 2000s.Adults of B. siliquastri are most easily collected by beating flowers, pods and foliage of Cercis from May to August, but they can also be reared from pods collected in spring.Stojanova et al. (2011) observed a large parasitoid fauna associated with Bruchidius siliquastri in Bulgaria, but no species of Hymenoptera have been reared from the London population of this beetle so far.The only other herbivorous insect recorded feeding on the trees was the jumping plant louse Cacopsylla pulchella (Löw) (Hemiptera: Psyllidae).
Bruchidius siliquastri can immediately be recognised from nearly all other species of Bruchinae occurring in Northern Europe by its bright red abdomen.This is conspicuous when the beetle is on its back, but is also visible dorsally, since the red pygidium extends well beyond the apices of the elytra.Apart from this striking feature it resembles a slightly small example of the common Bruchidius villosus (Fabricius), being black with whitish pubescence on the dorsal surface.The only other European Bruchinae with a reddish abdomen is the cosmopolitan Acanthoscelides obtectus (Say), an occasional kitchen and warehouse pest associated with dried beans.Acanthoscelides can resemble a large Bruchidius when stored in ethanol, but immediately differs by the dense brownish vestiture of elytra and pronotum when alive or dry.It is also immediately recognisable by the sharp teeth on the hind femora, along with its broader shape (Duff, 2016).
The specimens used for the Darwin Tree of Life project were collected on 23 July 2021 by a small Natural History Museum team, conducting a survey of Wetherby Gardens at the request of Natural History Museum patrons Holly Smith and Neil Osborn.The beetles were beaten in large numbers from a small Judas Tree growing from the pavement near the entrance to Wetherby Garden Square, less than a mile from the original South Kensington locality (Barclay, 2014).

Genome sequence report
The genome was sequenced from one male Bruchidius siliquastri (Figure 1) collected from Wetherby Gardens, Kensington, London, UK (51.49, -0.18).A total of 57-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 26 missing joins or mis-joins and removed 6 haplotypic duplications, reducing the assembly length by 1.11% and the scaffold number by 44.83%, and increasing the scaffold N50 by 10.13%.
The final assembly has a total length of 375.6 Mb in 15 sequence scaffolds with a scaffold N50 of 39.9 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 (99.95%) of the assembly sequence was assigned to 11 chromosomallevel scaffolds, representing 9 autosomes and the X and Y sex chromosomes.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.

Genome annotation report
The Bruchidius siliquastri genome assembly (GCA_949316355.1)was annotated using the Ensembl rapid annotation pipeline at the European Bioinformatics Institute (EBI).The resulting annotation includes 18,096 transcribed mRNAs from 17,940 protein-coding genes (Table 1; https://rapid.ensembl.org/Bruchidius_siliquastri_GCA_949316355.1/Info/Index)..The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from head and thorax tissue of icBruSili1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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 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.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Bruchidius siliquastri assembly (GCA_949316355.1) in Ensembl Rapid Release at the EBI.

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

Doga Cedden
Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, Göttingen, Germany Barclay et al. report a high-quality genome assembly from Bruchidius siliquastri.The background information about the 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.The reported assembly is available in the provided depository.

I have a single suggestion:
The Bruchidius siliquastri is a bean weevil (Bruchinae).It would be easier for readers if bean weevil (in its English form) is mentioned at least once in the background.

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 methods.
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.

Liang Lü
Hebei Normal University, Shijiazhuang, China I have read the main text of the manuscript, which reports a recently described seed-beetle, Bruchidius siliquastri Delobel, 2007.It is a satisfying paper that publishes an NGS sequence with detailed description of the background of the sample information in taxonomy, biology, collection, etc.The authors kindly presented in this manuscript clear images that make their identification trustable.The workflows of sample preparation, DNA extraction, sequencing, assembly, and annotation are fine and acceptable, with a few points of imperfection: 1.I suggest the authors integrate the duplicated descriptions (in the Genome sequence report and the Methods) of the sample information.
2. The authors refer the sequenced part of the sample is the "tissue from the abdomen", which tissue(s) were isolated for sequencing, muscle or gut or all of soft tissues?If the authors used the later two, how did they do with the DNA of dwelling microbes?
3. The use of BRAKER2, a pipeline includes many tools, seemed not to be as fully described as the programs used in previous procedures.

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: rove beetle taxonomy and molecular evolution

Figure 1 .
Figure 1.Photographs of Bruchidius siliquastri: a) A specimen collected in Kensington in 2014: photograph by Harry Taylor (Natural History Museum); b)-d) The specimen used for genome sequencing (icBruSili1): b) dorsal view, c) lateral view and d) ventral view.

Figure 2 .
Figure 2. Genome assembly of Bruchidius siliquastri, icBruSili1.1: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 375,583,928 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 (49,182,353 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (39,857,073 and 26,473,722 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/CASGFI01/dataset/CASGFI01/snail.

Figure 3 .
Figure 3. Genome assembly of Bruchidius siliquastri, icBruSili1.1: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/CASGFI01/dataset/CASGFI01/blob.

Figure 4 .
Figure 4. Genome assembly of Bruchidius siliquastri, icBruSili1.1: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/CASGFI01/dataset/CASGFI01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Bruchidius siliquastri, icBruSili1.1:Hi-C contact map of the icBruSili1.1 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=ff3I2oGrSVaZWymS1fyS7w.

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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.