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Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

38618196
10.12688/wellcomeopenres.19434.1
Data Note
Articles
The genome sequence of a cockchafer, Melolontha melolontha (Linnaeus, 1758)
[version 1; peer review: 2 approved, 2 approved with reservations]

Ashworth Mike Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 1
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life programme
Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Independent researcher, Yeovil, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

17 5 2023
2023
8 2222 5 2023
Copyright: © 2023 Ashworth M et al.
2023
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 male Melolontha melolontha (a cockchafer; Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence is 1,656.9 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,392 protein coding genes.

Melolontha melolontha
a Cockchafer
genome sequence
chromosomal
Coleoptera
Wellcome Trust206194 Wellcome Trust218328 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; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Scarabaeiformia; Scarabaeidae; Melolonthinae; Melolontha; Melolontha melolontha (Linnaeus, 1758) (NCBI:txid7061).

Background

The beetle Melolontha melolontha (Linnaeus, 1758) (Coleoptera: Scarabaeidae) is one of several members of the genus commonly known in English as the Cockchafer or May Bug. The name ‘melolontha’ originates from the ancient Greek for ‘fig-sheep’ because of the tendency for the beetle to feed on wild figs. It is widely distributed across Europe from the west coast to Ukraine and Turkey in the east, and as far north as southern Scandinavia. It was formerly found in large numbers. Populations have been drastically reduced due to changes in land use and the widespread use of insecticides but have been recovering since the 1980s. In the United Kingdom, it remains locally common in England and Wales with a few scattered records in Scotland.

Cockchafers are large and distinctive enough to make an impression in the public consciousness ( Figure 1), appearing in popular art, including paintings, opera, postcards, greeting cards and stamps, and as novelty chocolates ( Jones, 2018).

Figure 1. Melolontha melolontha (Linnaeus, 1758), European Cockchafer, to light trap, Yeovil, Somerset, United Kingdom, 30/31 May 2021.

Photograph by Mike Ashworth.

The larvae of M. melolontha feed on roots, taking about three years to develop to pupation. They can cause heavy damage to grasslands, fruit plantations and vineyards. In addition, the adults feed voraciously on the leaves of broadleaf trees, usually oak. In Central Europe the species has been regarded as an agricultural and horticultural pest. A range of control methods have been applied ( Malusá et al., 2020), including the use of biological control agents, such as the entomopathogenic fungus Beauveria brongniartii ( Kessler et al., 2004) and nematodes ( Erbaş et al., 2014).

The specimen used for genome assembly was an adult male. Male cockchafers are known to be strongly attracted to light, and this one flew into a dwelling one warm spring evening on the 20 May 2020 in a rural village in Somerset, south-west England. The high-quality genome sequence for a male M. melolontha reported here has been generated as part of the Darwin Tree of Life project. It will aid in understanding the biology, physiology and ecology of the species.

Genome sequence report

The genome was sequenced from one male Melolontha melolontha specimen collected from Yeovil, Somerset, UK (latitude 50.97, longitude –2.68). A total of 33-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 eight missing joins or mis-joins and removed four haplotypic duplications, reducing the assembly length by 0.15% and the scaffold number by 8.33%, and increasing the scaffold N50 by 1.14%.

The final assembly has a total length of 1,656,9 Mb in 55 sequence scaffolds with a scaffold N50 of 180.5 Mb ( Table 1). Most (99.46%) of the assembly sequence was assigned to 10 chromosomal-level scaffolds, representing 9 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 2– 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.

Table 1. Genome data for Melolontha melolontha, icMelMelo1.2.

Project accession data	
Assembly identifier	icMelMelo1.2	
Species	Melolontha melolontha	
Specimen	icMelMelo1	
NCBI taxonomy ID	7061	
BioProject	PRJEB50973	
BioSample ID	SAMEA7524378	
Isolate information	icMelMelo1, male; thorax (DNA sequencing); abdomen (RNA sequencing),
head and thorax (Hi-C scaffolding)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	60.8	≥ 50	
k-mer completeness	100%	≥ 95%	
BUSCO **	C:98.9%[S:97.4%,D:1.6%],
F:0.6%,M:0.5%,n:2,124	C ≥ 95%	
Percentage of assembly mapped to chromosomes	99.46%	≥ 95%	
Sex chromosomes	X chromosome	localised homologous pairs	
Organelles	Mitochondrial genome assembled.	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR8705878–ERR8705880	
Hi-C Illumina	ERR8702810, ERR8702811, ERR8702812	
PolyA RNA-Seq Illumina	ERR10378008	
Genome assembly	
Assembly accession	GCA_935421215.2	
Accession of alternate haplotype	GCA_935421255.1	
Span (Mb)	1,656.9	
Number of contigs	563	
Contig N50 length (Mb)	5.9	
Number of scaffolds	55	
Scaffold N50 length (Mb)	180.5	
Longest scaffold (Mb)	253.6	
Genome annotation	
Number of protein-coding genes	17,392	
Number of non-coding genes	4,888	
Number of gene transcripts	33,543	
* 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 v5.3.2. 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/icMelMelo1.2/dataset/CAKXYW02/busco.

Figure 2. Genome assembly of Melolontha melolontha, icMelMelo1.2: 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 1,656,884,372 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 (253,604,678 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (180,468,607 and 119,236,436 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/icMelMelo1.2/dataset/CAKXYW02/snail.

Figure 3. Genome assembly of Melolontha melolontha, icMelMelo1.2: 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/icMelMelo1.2/dataset/CAKXYW02/blob.

Figure 4. Genome assembly of Melolontha melolontha, icMelMelo1.2: 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/icMelMelo1.2/dataset/CAKXYW02/cumulative.

Figure 5. Genome assembly of Melolontha melolontha, icMelMelo1.2: Hi-C contact map of the icMelMelo1.2 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=WECRWt5cQgWcBCspo4Qc0g.

Table 2. Chromosomal pseudomolecules in the genome assembly of Melolontha melolontha, icMelMelo1.

INSDC accession	Chromosome	Size (Mb)	GC%	
OW285235.1	1	253.61	32.9	
OW285236.1	2	244.18	32.9	
OW285237.1	3	205.25	32.9	
OW285238.1	4	180.47	32.9	
OW285239.1	5	178.43	32.9	
OW285240.1	6	145.42	32.7	
OW285241.1	7	139.93	33.3	
OW285242.1	8	132.34	33	
OW285243.1	9	119.24	32.9	
OW285244.1	X	47.79	32.6	
OW285245.2	MT	0.02	28.3	
-	unplaced	10.22	38.7	

The estimated Quality Value (QV) of the final assembly is 60.8 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 98.9% (single = 97.4%, duplicated = 1.6%), using the endopterygota_odb10 reference set ( n = 2,124).

Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/7061.

Genome annotation report

The M. melolontha genome assembly (GCA_935421215.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Melolontha_melolontha_GCA_935421215.1/Info/Index). The resulting annotation includes 33,543 transcribed mRNAs from 17,392 protein-coding and 4,888 non-coding genes.

Methods

Sample acquisition and nucleic acid extraction

A male Melolontha melolontha specimen (icMelMelo1) was collected from Yeovil, Somerset, UK (latitude 50.97, longitude –2.68) on 20 May 2020. The specimen came to light from a rural garden and was collected by Mike Ashworth (independent researcher). The specimen was identified by the collector and preserved on dry ice.

The sample was prepared and DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The icMelMelo1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. 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.

RNA was extracted from abdomen tissue of icMelMelo1 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer’s instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration 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 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 were 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 head and thorax tissue of icMelMelo1 using the Arima2 kit and sequenced on the HiSeq X Ten 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 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., 2022), 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	4.0.7	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	yahs-1.1.91eebc2	https://github.com/c-zhou/yahs	

Genome annotation

The Ensembl gene annotation system ( Aken et al., 2016) was used to generate annotation for the Melolontha melolontha assembly (GCA_935421215.1). Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt ( UniProt Consortium, 2019).

Ethics and compliance issues

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. 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. All efforts are undertaken to minimise the suffering of animals used for sequencing. 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: Melolontha melolontha (cockchafer). Accession number PRJEB50973; https://identifiers.org/ena.embl/PRJEB50973 ( Wellcome Sanger Institute, 2022).

The genome sequence is released openly for reuse. The Melolontha melolontha 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 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 programme are listed here: https://doi.org/10.5281/zenodo.4783585.

Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.

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.21530.r77530
Reviewer response for version 1
Ragionieri Lapo 1Referee https://orcid.org/0000-0003-0099-2719

1 University of Cologne, Cologne, Germany
4 9 2024 Copyright: © 2024 Ragionieri L
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-with-reservations
The data note titled "The genome sequence of a cockchafer, Melolontha melolontha (Linnaeus, 1758)" by Mike Ashworth describes the sequencing and genome assembly of Melolontha melolontha. The authors utilized long-read sequencing technology (PacBio) to produce an initial assembly, which was subsequently scaffolded using Hi-C, resulting in a genome assembly at the chromosome level, with nearly all scaffolds assigned to chromosomes. The genome sequence of the cockchafer, Melolontha melolontha, represents a significant contribution to the fields of entomology and genomics. The genome assembly has a total length of 1,656 Mb across 55 sequence scaffolds, with a scaffold N50 of 180.5 Mb. There are some discrepancies between the text and the tables that should be corrected. The genome annotation includes 33,543 transcribed mRNAs, comprising 17,392 protein-coding genes and 4,888 non-coding genes.

The presentation of the results is well done, but the authors did not report any information about the masking of the genome.

Below are some specific comments and suggestions: Scale Bar: A scale bar is missing in Figure 1.

Keywords: The keywords should be distinct from the title to be effective.

Species Identification: The authors should cite the literature used for species identification.

Mitochondrial Genome: I strongly recommend submitting the mitochondrial genome separately with an independent accession number. Moreover, while the authors described the methods, they did not provide information about the mitochondrial genome annotation (coding genes, rRNAs, and tRNAs). It is expected that the authors submit the annotations obtained by MITOS separately.

Annotation: The authors should identify and quantify the transposable elements in the genome.

Command Lines: It is common practice to include the command lines used with all software. Providing this information would be very useful for readers.

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?

Partly

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Transcriptomic genomics proteomics

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.

10.21956/wellcomeopenres.21530.r77527
Reviewer response for version 1
Morino Yoshiaki 1Referee
1 Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
12 4 2024 Copyright: © 2024 Morino 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 authors present the genome sequence of a cockchafer, Melolontha melolontha. The constructed genome assembly was 1,656,9 Mb in 55 sequence scaffolds. Those sequences can be assigned to 10 chromosome-level scaffolds, including the X sex chromosome. Using Ensembl rapid annotation pipeline, 17,392 protein-coding genes were predicted. Assembly metrics meet benchmarks and are of sufficiently high quality. Therefore, this genomic data will facilitate the development of physiological and ecological studies of this or related species.

I only have two minor comments as below.

1. A description of what tissues and organs the "abdominal tissue" for RNA-seq actually contains would improve its future availability.

2. In relation to the identification of sex chromosomes, I would recommend that information on the sex determination mechanisms or sex chromosomes of this or related species be described in the background.

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:

Marine invertebrate, Evo-Devo

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.21530.r77529
Reviewer response for version 1
Garner Beulah 1Referee https://orcid.org/0000-0002-5229-2450

1 Natural History Museum, London, England, UK
11 4 2024 Copyright: © 2024 Garner B
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
In this data note, the authors present the genome assembly of Melolontha melolontha, the European cockchafer. The assembly consist of 10 chromosome scaffolds which is concurrent with other studies of this kind within the Scarabaeoidea.

The latest methods for genome sequencing, assembly, annotation and characterization used in this study are standardized across the Darwin Tree of Life Consortium, being clearly and methodically described here. Sequencing assembly is clearly supplemented with the appropriate illustrations. The standard for generating high quality genome assemblies is high, therefore this genome sequence is a valuable resource for studies into the systematics of this species as well as its relatives.

As a curiosity, why was DNA and RNA extracted from different parts of the beetle (Johnson, et al., 2013 [Ref 1]).

The title should be clear this is the European cockchafer and in fact a beetle (Coleoptera). Consistency in reporting the species name, author and year. Cite the original publication (Wägele,  et al., 2011[Ref 2]). 

I would like to see references for the statements on M. melolontha decline and for it's recovery since the 1980s to improve the overall rationale.

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:

Coleoptera taxonomy and systematics.

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.21530.r77533
Reviewer response for version 1
Alqahtani Fahad 1Referee https://orcid.org/0000-0002-2498-4871

1 King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
27 3 2024 Copyright: © 2024 Alqahtani F
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-with-reservations
The authors have achieved a highly complete genome assembly at the chromosome level and provided high-quality annotation for an adult male cockchafer,  Melolontha melolontha (Linnaeus, 1758). The genome assembly utilized three sequencing technologies: Pacific Biosciences SEQUEL II, Hi-C Illumina, and PolyA RNA-Seq Illumina. The completeness of the genome assembly was assessed using BUSCO analysis, which indicated a genome size of 1,656.9 Mb, with 98.9% of common genes completely present. Figure 1 is very detailed, showcasing some features clearly.

However, minor comments should be addressed: In the "Genome Sequence Report," the authors have incorrectly stated the total length of the final assembly as "1,656,9 Mb"; this should be corrected to 1,656.9 Mb.

Also, in the "Genome Sequence Report" section, the authors state that the number of sequence scaffolds is 55, which differs from the 54 reported in NCBI. This difference may be due to the inclusion of the mitochondrial sequence; if so, the authors should clarify that the mitochondrial sequence is included. This adjustment should also be reflected in Table 1.

In Table 1, the authors report the number of contigs as 563, while NCBI lists 562.

"Pretext" in the Genome Assembly section should be corrected to "PretextView".

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:

Bioinformatics

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
==== Refs
Abdennur N Mirny LA : Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36 (1 ):311–316. 10.1093/bioinformatics/btz540 31290943
Aken BL Ayling S Barrell D : The Ensembl gene annotation system. Database (Oxford). 2016;2016 :baw093. 10.1093/database/baw093 27337980
Allio R Schomaker-Bastos A Romiguier J : MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20 (4 ):892–905. 10.1111/1755-0998.13160 32243090
Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69 (2 ):313–9. 10.1016/j.ympev.2012.08.023 22982435
Challis R Richards E Rajan J : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10 (4 ):1361–1374. 10.1534/g3.119.400908 32071071
Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18 (2 ):170–175. 10.1038/s41592-020-01056-5 33526886
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
Erbaş Z Gokce C Hazir S : Isolation and identification of entomopathogenic nematodes (Nematoda: Rhabditida) from the Eastern Black Sea region and their biocontrol potential against Melolontha melolontha (Coleoptera: Scarabaeidae) larvae. Turk J Agric For. 2014;38 (2 ):187–197. 10.3906/tar-1301-42
Guan D McCarthy SA Wood J : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36 (9 ):2896–2898. 10.1093/bioinformatics/btaa025 31971576
Harry E : PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps. 2022; (Accessed: 19 October 2022). Reference Source
Howe K Chow W Collins J : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10 (1 ):giaa153. 10.1093/gigascience/giaa153 33420778
Jones R : Beetles.Collins New Naturalist Library,2018.
Kerpedjiev P Abdennur N Lekschas F : HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19 (1 ):125. 10.1186/s13059-018-1486-1 30143029
Kessler P Enkerl J Schweize C : Survival of Beauveria brongniartii in the soil after application as a biocontrol agent against the European cockchafer Melolontha melolontha. BioControl. 2004;49 (5 ):563–581. 10.1023/B:BICO.0000036441.40227.ed
Malusá E Tartanus M Furmanczyk EM : Holistic approach to control Melolontha spp. in organic strawberry plantations. Org Agr. 2020;10 (Suppl 1 ):13–22. 10.1007/s13165-020-00295-2
Manni M Berkeley MR Seppey M : BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38 (10 ):4647–4654. 10.1093/molbev/msab199 34320186
Rao SSP Huntley MH Durand NC : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159 (7 ):1665–80. 10.1016/j.cell.2014.11.021 25497547
Rhie A McCarthy SA Fedrigo O : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592 (7856 ):737–746. 10.1038/s41586-021-03451-0 33911273
Rhie A Walenz BP Koren S : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology. 2020;21 (1 ):245. 10.1186/s13059-020-02134-9 32928274
Simão FA Waterhouse RM Ioannidis P : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31 (19 ):3210–2. 10.1093/bioinformatics/btv351 26059717
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0).Zenodo. 2023a; (Accessed: 17 April 2023). 10.5281/zenodo.7755665
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev).Zenodo. 2023b; (Accessed: 17 April 2023). 10.5281/zenodo.6785935
Uliano-Silva M Ferreira JGRN Krasheninnikova K : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads. bioRxiv. [Preprint],2022. 10.1101/2022.12.23.521667
UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47 (D1 ):D506–D515. 10.1093/nar/gky1049 30395287
Vasimuddin Md Misra S Li H : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).IEEE,2019;314–324. 10.1109/IPDPS.2019.00041
Wellcome Sanger Institute: The genome sequence of a cockchafer, Melolontha melolontha (Linnaeus, 1758). European Nucleotide Archive.[dataset], accession number PRJEB50973,2022.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. Edited by C. Alkan,2023;39 (1 ):btac808. 10.1093/bioinformatics/btac808 36525368
