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Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
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10.12688/wellcomeopenres.20841.1
Data Note
Articles
The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775)
[version 1; peer review: 2 approved]

Boyes Douglas Investigation Resources 1
Januszczak Inez Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0003-3857-9989
2
Lees David C. Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-7580-8560
2
University of Oxford and Wytham Woods 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 UK Centre for Ecology & Hydrology, Wallingford, England, UK
2 Natural History Museum, London, England, UK
a mark.blaxter@sanger.ac.uk
+ Deceased author

No competing interests were disclosed.

29 2 2024
2024
9 969 1 2024
Copyright: © 2024 Boyes D 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 male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.

Lomographa bimaculata
white-pinioned spotted
genome sequence
chromosomal
Lepidoptera
Wellcome Trust218328 206194 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Geometroidea; Geometridae; Ennominae; Lomographa; Lomographa bimaculata (Fabricius, 1775) (NCBI:txid393326).

Background

Lomographa bimaculata, or the White-pinion Spotted, is the type species of the genus Lomographa, originally described as Geometra taminata [Denis & Schiffermüller], 1775, now a synonym of L. bimaculata (Fabricius, 1775). The White-pinion Spotted has an adult wingspan of 22–26 mm (about 13–14 mm forewing length; Waring et al., 2017). The adults are nocturnal. The caterpillars are greenish with a purplish-red dorsal line, but they may vary in colour from a light yellow to a dark red through their various instars ( Buckler, 1897). The larvae feed on hawthorn ( Crataegus sp.) and blackthorn ( Prunus spinosa), and other Rosaceae shrubs ( Henwood et al., 2020; Leather, 1991), and the moth occurs in woodland open areas with such foodplants. Adults are nocturnal, with white background wings, distinguished by two black inverted triangular costal spots at the top of each convex dotted crossline. They fly from mid-April to mid-July in the UK with a peak in early June ( Randle et al., 2019).

L. bimaculata is common in most of the British Isles but very local in southern Scotland and Ireland ( Waring et al., 2017). It can be found in mainly woodland areas over most of Europe although absent in southern Spain and northern Scandinavia. Its distribution extends eastward through Russia and Central Asia to Japan ( GBIF Secretariat, 2023). Unlike many other UK moth species, L. bimaculata has been slightly increasing its range, with an annual population change increase over 35 years of 1% ( Conrad et al., 2006), yet from 1970 to 2016 its abundance declined by 23% ( Randle et al., 2019), and has been expanding northwards ( Waring et al., 2017).

Neighbour-joining trees for its DNA barcodes (BOLD, 15/12/2023) reveal that L. bimaculata (cluster number, BIN BOLD:AAB9407) has a mean pairwise divergence spanning 0.07% to 0.38% ( n = 40). L. bimaculata is a mitochondrially very isolated species, with no other Lomographa within the top 99 hit on BOLD (over 6.17 % distant to other geometrids). The other British Lomographa, L. temerata is around 9.8% pairwise divergent to it based on UK DNA barcodes. The species was treated in a multi-locus study by Murillo-Ramos et al. (2019), and belongs to the ennomine tribe Baptini, most closely related to the tribe Therini. The genome will be useful to further explore and revise the higher taxonomy of the genus.

We present a chromosomally complete genome sequence for the White-pinion Spotted ( Lomographa bimaculata) as part of the Darwin Tree of Life Project. This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago, encompassing Britain and Ireland.

Genome sequence report

The genome was sequenced from one male Lomographa bimaculata ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.32). A total of 48-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 3 missing joins or mis-joins and removed 1 haplotypic duplications, reducing the scaffold number by 2.94%.

Figure 1. Photograph of the Lomographa bimaculata (ilLomBima1) specimen used for genome sequencing.

The final assembly has a total length of 554.7 Mb in 32 sequence scaffolds with a scaffold N50 of 19.6 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 (99.99%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome. 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.

Table 1. Genome data for Lomographa bimaculata, ilLomBima1.1.

Project accession data	
Assembly identifier	ilLomBima1.1	
Species	Lomographa bimaculata	
Specimen	ilLomBima1	
NCBI taxonomy ID	393326	
BioProject	PRJEB58085	
BioSample ID	SAMEA10979145	
Isolate information	ilLomBima1
ilLomBima1	
Assembly metrics *	Benchmark	
Consensus quality (QV)	68.0	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:98.6%[S:98.0%,D:0.6%],
F:0.4%,M:1.0%,n:5,286	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	99.99%	≥ 95%	
Sex chromosomes	ZZ	localised homologous pairs	
Organelles	Mitochondrial genome: 16.66 kb	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10662030	
Hi-C Illumina	ERR10659259	
PolyA RNA-Seq Illumina	ERR11242511	
Genome assembly	
Assembly accession	GCA_948107665.1	
Accession of alternate haplotype	GCA_948107665.1	
Span (Mb)	554.7	
Number of contigs	68	
Contig N50 length (Mb)	14.2	
Number of scaffolds	32	
Scaffold N50 length (Mb)	19.6	
Longest scaffold (Mb)	27.52	
Genome annotation	
Number of protein-coding genes	12,749	
Number of non-coding genes	1,754	
Number of gene transcripts	22,526	
* 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 lepidoptera_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/CANUFC01/dataset/CANUFC01/busco.

Figure 2. Genome assembly of Lomographa bimaculata, ilLomBima1.1: 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 554,752,746 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 (27,520,313 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (19,622,098 and 13,309,989 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 lepidoptera_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANUFC01/dataset/CANUFC01/snail.

Figure 3. Genome assembly of Lomographa bimaculata, ilLomBima1.1: 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/CANUFC01/dataset/CANUFC01/blob.

Figure 4. Genome assembly of Lomographa bimaculata, ilLomBima1.1: 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/CANUFC01/dataset/CANUFC01/cumulative.

Figure 5. Genome assembly of Lomographa bimaculata, ilLomBima1.1: Hi-C contact map of the ilLomBima1.1 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=QsVq0YVKSwODyXqtnd55xQ.

Table 2. Chromosomal pseudomolecules in the genome assembly of Lomographa bimaculata, ilLomBima1.

INSDC accession	Chromosome	Length (Mb)	GC%	
OX403585.1	1	22.46	36.0	
OX403586.1	2	22.23	36.0	
OX403587.1	3	21.93	36.0	
OX403588.1	4	21.82	36.0	
OX403589.1	5	21.24	36.5	
OX403590.1	6	20.94	35.5	
OX403591.1	7	20.61	36.0	
OX403592.1	8	20.46	35.5	
OX403593.1	9	20.33	35.5	
OX403594.1	10	20.1	36.0	
OX403595.1	11	20.07	36.0	
OX403596.1	12	19.62	36.0	
OX403597.1	13	19.54	36.0	
OX403598.1	14	19.14	36.0	
OX403599.1	15	18.92	36.0	
OX403600.1	16	18.55	36.0	
OX403601.1	17	18.26	36.0	
OX403602.1	18	17.82	36.5	
OX403603.1	19	17.79	36.5	
OX403604.1	20	17.16	36.0	
OX403605.1	21	17.01	36.5	
OX403606.1	22	14.73	36.5	
OX403607.1	23	14.36	37.0	
OX403608.1	24	14.25	36.5	
OX403609.1	25	13.31	36.5	
OX403610.1	26	12.61	36.5	
OX403611.1	27	10.84	38.5	
OX403612.1	28	10.84	37.0	
OX403613.1	29	10.13	37.5	
OX403614.1	30	10.12	37.0	
OX403584.1	Z	27.52	36.0	
OX403615.1	MT	0.02	18.0	

The estimated Quality Value (QV) of the final assembly is 68.0 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 98.6% (single = 98.0%, duplicated = 0.6%), using the lepidoptera_odb10 reference set ( n = 5,286).

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/393326.

Genome annotation report

The Lomographa bimaculata genome assembly (GCA_948107665.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Lomographa_bimaculata_GCA_948107665.1/Info/Index). The resulting annotation includes 23,526 transcribed mRNAs from 12,749 protein-coding and 1,754 non-coding genes.

Methods

Sample acquisition and nucleic acid extraction

A male Lomographa bimaculata (specimen ID Ox001884, ToLID ilLomBima1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude –1.32) on 2021-05-28 using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.

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 ilLomBima1 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the head and thorax was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).

HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol ( Oatley et al., 2023). The DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): 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.

RNA was extracted from abdomen tissue of ilLomBima1 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

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 was 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 remaining head and thorax tissue of ilLomBima1 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 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.

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	4.2.1	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 Ensembl Genebuild annotation system ( Aken et al., 2016) was used to generate annotation for the Lomographa bimaculata assembly (GCA_948107665.1). 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).

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: Lomographa bimaculata (white-pinion spotted). Accession number PRJEB58085; https://identifiers.org/ena.embl/PRJEB58085 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Lomographa bimaculata 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 University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.

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.23060.r90111
Reviewer response for version 1
Ortiz Antonio 1Referee
1 University of Murcia, Murcia, Spain
9 9 2024 Copyright: © 2024 Ortiz A
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
Boyes, Januszczak & Lees describes the genome assembly of Lomographa bimaculata and provides important genomic information about its size (near 555 Mb) in 31 chromosomes. A new genome sequenced from the moth family Geometridae is added to others species of the family as Thera britannica (Turner, 1925) by Boyes & Holland (2023), Eupithecia vulgata (Haworth, 1809) by Boyes & Mulley (2023), Eupithecia insigniata (Hübner, 1790) by Holland (2023), Eulithis prunata (Linnaeus, 1758) by Boyes & Holland (2023) all published in Wellcome Open Research (WOR). This assembly provides valuable information for the genomics of Lepidoptera and for further phylogenetic research in the evolutionary pattern in Lepidoptera.

The methods for the sequencing and assembly used are appropriate and technically supported.

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:

Systematics and Evolution of Lepidoptera and other insects

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.23060.r86951
Reviewer response for version 1
Ignacimuthu Savarimuthu 1Referee
Kuppusamy Sivasankaran 2Co-referee
1 St. Xavier's College, Interdisciplinary Research Centre in Biology, Xavier Research Foundation, Manonmaniam Sundaranar University, Thirunelveli, TN, India
2 Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
16 7 2024 Copyright: © 2024 Ignacimuthu S and Kuppusamy S
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 have assembled and annotated of  Lomographa bimaculata (Fabricius, 1775) genomic sequence. They sequenced about 554.7 mega bases of the assembled genome using 32 scaffolds. Total of 12, 749 protein coding genes, 1,754 non-coding genes and the largest number of gene transcripts (22,526) have been observed through genome annotation. Standard techniques have been employed to isolate DNA, and the relevant software has been used for sequence assembly and annotation.

Comments on the manuscript The authors have constantly given the complete form of the genus name  Lomographa bimaculata’s in the article. The genus name may be presented in full the first time, and then in abbreviated form later on, such as  L. bimaculata.  

The first paragraph of the background the third sentence “The adults are nocturnal” may be deleted. Because the same meaning was provided in the penultimate sentence of the first paragraph.

In the fourth sentence of the first paragraph the last line authors have given “foodplants”. It’s not a single word. It can be separated i.e., food plants.

The mitochondrial genome was annotated but the exact number of mitochondrial genome sequence lengths was not mentioned in the text. The mitogenome length can be given in the text.

Table number and title for table 3 was given in between the text in page number 9. I think it is wrongly placed. The table number and title can be deleted or replaced. 

Above all, I confirm that the manuscript meets the necessary scientific standard and is suitable for indexing.

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:

Molecular Biology

We confirm that we have read this submission and believe that we 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.
==== 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
Bates A Clayton-Lucey I Howard C : Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor ®3 for LI PacBio. protocols.io. 2023. 10.17504/protocols.io.81wgbxzq3lpk/v1
Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69 (2 ):313–319. 10.1016/j.ympev.2012.08.023 22982435
Buckler W : The Larvæ of the British Butterflies and Moths.Ray Society,1897;7 .
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
Conrad KF Warren MS Fox R : Rapid declines of common, widespread British moths provide evidence of an insect biodiversity crisis. Biol Conserv. 2006;132 (3 ):279–291. 10.1016/j.biocon.2006.04.020
Denton A Oatley G Cornwell C : Sanger Tree of Life Sample Homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1
Denton A Yatsenko H Jay J : Sanger Tree of Life Wet Laboratory Protocol Collection V.1. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
do Amaral RJV Bates A Denton A : Sanger Tree of Life RNA Extraction: Automated MagMax™ mirVana. protocols.io. 2023. 10.17504/protocols.io.6qpvr36n3vmk/v1
GBIF Secretariat: Lomographa bimaculata (Fabricius, 1775). GBIF Backbone Taxonomy ,2023; [Accessed 31 December 2023]. Reference Source
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
Henwood B Sterling P Lewington R : Field Guide to the Caterpillars of Great Britain and Ireland.London: Bloomsbury,2020. 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
Jay J Yatsenko H Narváez-Gómez JP : Sanger Tree of Life Sample Preparation: Triage and Dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1
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
Leather SR : Feeding Specialisation and Host Distribution of British and Finnish Prunus Feeding Macrolepidoptera. Oikos. 1991;60 (1 ):40–48. 10.2307/3544990
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
Murillo-Ramos L Brehm G Sihvonen P : A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies. PeerJ. 2019;7 : e7386. 10.7717/peerj.7386 31523494
Oatley G Denton A Howard C : Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2. protocols.io. 2023. 10.17504/protocols.io.kxygx3y4dg8j/v1
Randle Z Evans-Hill LJ Parsons MS : Atlas of Britain & Ireland’s Larger Moths. Newbury: NatureBureau,2019. Reference Source
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 ):1665–1680. 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 Biol. 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 ):3210–3212. 10.1093/bioinformatics/btv351 26059717
Strickland M Cornwell C Howard C : Sanger Tree of Life Fragmented DNA clean up: Manual SPRI. protocols.io. 2023. 10.17504/protocols.io.kxygx3y1dg8j/v1
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a; [Accessed 21 July 2023]. 10.5281/zenodo.7755665
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b; [Accessed 21 July 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. BMC Bioinformatics. 2023;24 (1 ): 288. 10.1186/s12859-023-05385-y 37464285
UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47 (D1 ):D506–D515. 10.1093/nar/gky1049 30395287
Vasimuddin M 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
Waring P Townsend M Lewington R : Field Guide to the Moths of Great Britain and Ireland: Third Edition. Bloomsbury Wildlife Guides,2017. Reference Source
Wellcome Sanger Institute: The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775) European Nucleotide Archive.[dataset], accession number PRJEB58085,2023.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
