
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
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10.12688/wellcomeopenres.22422.1
Data Note
Articles
The genome sequence of a soldier beetle, Cantharis flavilabris Fallén, 1807
[version 1; peer review: 2 approved, 1 not approved]

Barclay Maxwell V. L. Investigation Resources https://orcid.org/0000-0003-4989-2014
1
Natural History Museum Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Natural History Museum, London, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

11 6 2024
2024
9 30316 5 2024
Copyright: © 2024 Barclay MVL et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a genome assembly from an individual female Cantharis flavilabris (soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence is 348.3 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 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,711 protein coding genes.

Cantharis flavilabris
soldier beetle
genome sequence
chromosomal
Coleoptera
Wellcome Trust218328 206194 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Elateroidea; Cantharidae; Cantharinae; Cantharis; Cantharis flavilabris Fallén, 1807 (NCBI:txid877752).

Background

The genome of the soldier beetle, Cantharis flavilabris, 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 Cantharis flavilabris, based on one female specimen from Leith Hill, England, UK.

Genome sequence report

The genome was sequenced from one female Cantharis flavilabris ( Figure 1) collected from Leith Hill, England, UK (51.18, –0.37). A total of 74-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 16 missing joins or mis-joins and removed 5 haplotypic duplications, reducing the assembly length by 0.60% and the scaffold number by 6.90%, and increasing the scaffold N50 by 11.36%.

Figure 1. Photograph of the Cantharis flavilabris (icCanFlav1) specimen used for genome sequencing.

The final assembly has a total length of 348.3 Mb in 26 sequence scaffolds with a scaffold N50 of 47.5 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 (99.8%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds, representing 6 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). Chromosome X was assigned by synteny to Cantharis rufa (GCA_947369205.1) ( Sivell et al., 2023) and Cantharis rustica (GCA_911387805.1) ( Sivell et al., 2021). 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.

Table 1. Genome data for Cantharis flavilabris, icCanFlav1.1.

Project accession data	
Assembly identifier	icCanFlav1.1	
Species	Cantharis flavilabris	
Specimen	icCanFlav1	
NCBI taxonomy ID	877752	
BioProject	PRJEB59137	
BioSample ID	SAMEA111458455	
Isolate information	icCanFlav1, female: thorax (DNA sequencing), head
(Hi-C sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	66.2	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:98.7%[S:96.1%,D:2.6%],
F:0.6%,M:0.7%,n:2,124	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	99.8%	≥ 95%	
Sex chromosomes	X	localised
homologous pairs	
Organelles	Mitochondrial genome: 17.5 kb	complete single
alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10809391	
Hi-C Illumina	ERR10802468	
Genome assembly	
Assembly accession	GCA_949152465.1	
Accession of alternate haplotype	GCA_949152385.1	
Span (Mb)	348.3	
Number of contigs	84	
Contig N50 length (Mb)	10.5	
Number of scaffolds	26	
Scaffold N50 length (Mb)	47.5	
Longest scaffold (Mb)	106.12	
Genome annotation	
Number of protein-coding genes	22,711	
Number of gene transcripts	23,081	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).

** BUSCO scores based on the endopterygota_odb10 BUSCO set using version 5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/CASCJT01/dataset/CASCJT01/busco.

Figure 2. Genome assembly of Cantharis flavilabris, icCanFlav1.1: 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 348,304,867 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 (106,117,081 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (47,548,398 and 33,898,588 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/CASCJT01/dataset/CASCJT01/snail.

Figure 3. Genome assembly of Cantharis flavilabris, icCanFlav1.1: 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/CASCJT01/dataset/CASCJT01/blob.

Figure 4. Genome assembly of Cantharis flavilabris, icCanFlav1.1: 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/CASCJT01/dataset/CASCJT01/cumulative.

Figure 5. Genome assembly of Cantharis flavilabris, icCanFlav1.1: Hi-C contact map of the icCanFlav1.1 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=Kkxirt3sTYK9ripEyx-0Yw.

Table 2. Chromosomal pseudomolecules in the genome assembly of Cantharis flavilabris, icCanFlav1.

INSDC
accession	Chromosome	Length
(Mb)	GC%	
OX424435.1	1	106.12	30.5	
OX424436.1	2	56.15	31.5	
OX424437.1	3	47.55	33.5	
OX424438.1	4	42.28	31.5	
OX424439.1	5	34.3	32.0	
OX424440.1	6	33.9	32.5	
OX424441.1	X	27.33	31.5	
OX424442.1	MT	0.02	21.0	

The estimated Quality Value (QV) of the final assembly is 66.2 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 98.7% (single = 96.1%, duplicated = 2.6%), using the endopterygota_odb10 reference set ( n = 2,124).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/877752.

Genome annotation report

The Cantharis flavilabris genome assembly (GCA_949152465.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Cantharis_flavilabris_GCA_949152465.1/Info/Index). The resulting annotation includes 23,081 transcribed mRNAs from 22,711 protein-coding genes.

Methods

Sample acquisition and nucleic acid extraction

A female Cantharis flavilabris (specimen ID NHMUK014439758, ToLID icCanFlav1) was collected from Leith Hill, England, UK (latitude 51.18, longitude –0.37) on 2021-06-20. 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 WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the icCanFlav1 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the thorax was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a). HMW DNA was extracted using the Automated MagAttract v1 protocol ( Oatley et al., 2023a). HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30 ( Todorovic et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Oatley et al., 2023b): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io ( Denton et al., 2023b).

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 tissue of icCanFlav1 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 HiGlass ( Kerpedjiev et al., 2018) and PretextView ( 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.

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) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software
tool	Version	Source	
BlobToolKit	4.1.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
sanger-tol/
genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/
readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
YaHS	1.2a	https://github.com/c-zhou/yahs	

Genome annotation

The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Cantharis flavilabris assembly (GCA_949152465.1) 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.

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)

Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.

Data availability

European Nucleotide Archive: Cantharis flavilabris. Accession number PRJEB59137; https://identifiers.org/ena.embl/PRJEB59137 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Cantharis flavilabris genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7139035.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.24701.r90895
Reviewer response for version 1
Villoutreix Romain 1Referee
1 Universite de Montpellier, Montpellier, Occitanie, France
13 9 2024 Copyright: © 2024 Villoutreix R
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
Barclay and colleagues present a genome assembly for the soldier beetle Cantharis flavilabris.

Great care was taken in identifying an individual of the target species and producing this assembly.

The authors used cutting edge data and pipelines to produce an excellent chromosomal level assembly. This ressource will be of great use to perform genomic work in this species.

I therefore recommend this article.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Evolutionary 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.

10.21956/wellcomeopenres.24701.r87914
Reviewer response for version 1
Nash Will 1Referee https://orcid.org/0000-0002-6790-1167

1 Research Faculty, Earlham Institute, Norwich Research Park, Norwich, England, UK
6 8 2024 Copyright: © 2024 Nash W
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationreject
The genome of a soldier beetle is presented. It is sequenced from 74x of PacBioHifi and scaffolded with Hi-C.

The assembly is 348.3 Mb over 26 scaffolds with an N50 of 47.5Mb. 23,081 genes are annotated. 

It is dissapointing to see no background included. This does not provide any detail on this species or the biological context of this assembly. 

The methods are cutting edge in line with other DToL genomes. The Hi-C protocol is not repeatable, and as such I cannot recommend this manuscript.

Are sufficient details of methods and materials provided to allow replication by others?

No

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genome assembly, population genomics, bioinformatics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

10.21956/wellcomeopenres.24701.r89176
Reviewer response for version 1
Wang Yangzi 1Referee https://orcid.org/0000-0003-2146-515X

1 University of Mainz, Mainz, Germany
6 8 2024 Copyright: © 2024 Wang Y
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The manuscript titled "The genome sequence of a soldier beetle, Cantharis flavilabris Fallén, 1807" presents a high-quality genome assembly for the soldier beetle, Cantharis flavilabris. The authors have employed a combination of robust methodological frameworks that include third-generation long-read sequencing technology, Hi-C, rigorous data curation, and reliably automated gene annotation processes. Below is a detailed evaluation of the manuscript.

The project demonstrates a high level of professionalism. The genome data has been deposited in NCBI and EMBL, ensuring transparency and easy accessibility. The accessibility of the genome assembly and the raw data has been verified, confirming that it matches the descriptions provided in the manuscript. The authors have utilized a combination of PacBio HiFi long reads and Hi-C data to achieve a high-quality assembly. Manual curation further improved the assembly by correcting missing joins and removing haplotypic duplications. This approach has resulted in a polished genome sequence. The evaluation shows the genome assembly presented is of high quality, with several key measures highlighting its completeness and accuracy: 348.3 Mb genome span; 47.5 Mb Scaffold N50; Chromosome-level assembly; 98.7% BUSCO Completeness. These data suggest that the assembly is complete and highly contiguous, providing a reliable reference genome for further studies. In addition to the nuclear genome, the mitochondrial genome was also assembled, measuring 17.5 kb in length. This presents another valuable genetic dataset for the species. The Ensembl rapid annotation pipeline was employed to annotate the genome, resulting in the identification of 22,711 protein-coding genes. This automated process ensures consistency and accuracy in gene prediction, which paves the way for further functional genomics studies. Furthermore, the manuscript includes detailed figures illustrating the genome assembly statistics, scaffold distribution, and other key aspects.

There is a minor error in the manuscript: the raw data identifiers ERR10809391 and ERR10802468 appear to be from NCBI SRA, not INSDC, as mentioned. I only found the data using these accession numbers on NCBI. Please correct this in the manuscript. Additionally, I recommend including both accession numbers in the Data Availability section to facilitate quick data access for readers.

In conclusion, this manuscript represents a valuable genomic dataset of the soldier beetle for the research community. The authors have produced a high-quality genome assembly for the soldier beetle using cutting-edge sequencing technologies and stringent data curation. The availability of this genome assembly in public databases, along with the comprehensive methodological details provided, ensures that this work will be a valuable resource for future research. The authors are to be commended for their professionalism and the high standards of their work.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genomics, population genomics, epigenomics

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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