The genome sequence of the double-striped pug, Gymnoscelis rufifasciata (Haworth, 1809)

We present a genome assembly from an individual female Gymnoscelis rufifasciata (the double-striped pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 352 megabases in span. The majority of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 15.4 kilobases in length.


Background
The double-striped pug (Gymnoscelis rufifasciata), named after the two dark bands across its wings, is a moth of the family Geometridae.A typical adult's wingspan is 15 to 19 mm, with forewings varying from light brown to dark reddish-brown, and the intensity of its stripes also variable (Riley & Prior, 2003;Skinner & Wilson, 2009).A double brooded species, adults are first on the wing in the UK from March to May, although they have been observed as early as January in the mildest winters, and then again from July to August (Randle et al., 2019); they are frequently found in light traps throughout these periods.
Gymnoscelis rufifasciata is common across western and central Europe, and while it has long been common in southern England, observations in northern England and Scotland have increased dramatically since the year 2000 (Fox et al., 2021), likely caused by the increasing suitability of the climate due to rising average temperatures.Indeed, G. rufifasciata appears to be thriving in the current climate, and its abundance in Britain was reported to have increased 220% from 1986 to 2016 (Randle et al., 2019); its generalist habitat usage, which includes gardens, wasteland, heathland and hedgerows (Riley & Prior, 2003;Randle et al., 2019) is likely to have contributed to its recent success.Its larvae are polyphagous, and favoured food plants include gorse (Ulex), holly (Ilex) and heather (Calluna) (Riley & Prior, 2003;Skinner & Wilson, 2009).

Genome sequence report
The genome was sequenced from one female G. rufifasciata (Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.765, longitude -1.327).A total of 58-fold coverage in Pacific Biosciences single-molecule long reads and 102-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 11 missing/misjoins and removed 3 haplotypic duplications, reducing the assembly size by 0.54% and the scaffold number by 19.05%.
The final assembly has a total length of 462 Mb in 51 sequence scaffolds with a scaffold N50 of 15.6 Mb (Table 1).The majority of the assembly sequence (99.82%) was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes  DNA was extracted from whole organism tissue at the Wellcome Sanger Institute (WSI) Scientific Operations core from the whole organism using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.Pacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were constructed according to the manufacturers' instructions.Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II (HiFi) and Illumina HiSeq X (10X) instruments.Hi-C data were generated from head tissue of ilGymRufi2 using the Arima Hi-C+ kit and sequenced on an Illumina NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021); haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).One round of polishing was      Is the rationale for creating the dataset(s) clearly described?Yes

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Insect genome

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.
Background.There is no motivation for this study in the introduction.Nothing wrong is said, but the read has no idea why the work was done.Its perfectly fine that the work was done in the context of a large survey, but tell the reader that.Is its expansion north in the UK a problem or likely to become one?The paper is not about its ecology or morphology, but about its genetics.That is not mentioned once.
Genome Sequence Report.The BUSCO reference should be in the methods, not results section.Methods.I assume that the Hi-C library was constructed according to the manufacturer's specifications?
All parameter setting if they were different from default of each piece of bioinformatic software needs to be specified.Just put a sentence to begin that everything was default unless specified otherwise.What assessment was done to ensure that default was adequate?
Table 3 is of little to no value and contains much duplicated information.Just add the version numbers of software used inline at the appropriate places in the methods section.
Is the Ethics statement needed?It just says the provider of the sample should meet some standard, but does not actually say that they did in this case.Either drop the statement because there are no legal requirements for insect research beyond basic humane treatment or actually say the standard was met.
Add something to the report that contextualize the research for the reader.Is this species the first of a taxon to be assembled, is it an outgroup to some established model species, is it now possible to investigate some interesting aspect of the species biology, etc?This does not to be extensive or highly directed, but there is currently no justification of this work outside of the Data Availability Statement.Even Data Note should contain rationale for the work.

Is the rationale for creating the dataset(s) clearly described? No
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? No
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genome assembly & Annotation, Insects, Molecular Genetics 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. rufifasciata.
The review report from asks whether the rationale for creating the dataset is clearly described.Although no justification is provided within this note, the justification for the DToL project is clearly described elsewhere, and the assemblies, including the one reported here, are already being used as resources in other studies, demonstrating their value.
The introduction is entirely focused on the UK population.This is understandable given the origin of the sequenced specimen, but it would be helpful to a least mention the full extent of the species' range.
One important issue to address is that the abstract says the assembly length is 352 Mb but the main text and figures show that it is 462 Mb.

Henry North
University of Cambridge, Cambridge, UK Boyes et al. present a reference genome of Gymnoscelis rufifasciata, including both sex chromosomes and the mitochondrial genome.The quality of this assembly is high by all measures of completeness and contiguity.The methods are reported clearly and in detail.
These data will prove valuable in broader research efforts aimed at understanding chromosomal evolution during the radiation of the Lepidoptera, which requires assemblies from species that span the rich diversity of this order.Pugs such as this species are a familiar occurrence in British light traps and, as the authors point out, G. rufifasciata is noteworthy for its increased abundance over the past half-century.This assembly permits an investigation of relative population size change deeper in time -when we know what the climate looked like but have no census population size estimates -using coalescent-based demographic inference.The assembly will also be of use in research aimed at understanding the evolution of lepidopteran polyphagy using comparative genomics approaches.
This publicly available data is a testament to the efforts of the Tree of Life team, and to Douglas' contribution to the study and public appreciation of the full diversity of the Lepidoptera.
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: Population genomics, speciation, adaptation 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.

Figure 1 .
Figure 1.Image of the Gymnoscelis rufifasciata (ilGymRufi1) specimen taken prior to preservation and processing.Specimen shown next to FluidX storage tube, 43.9 mm in length.

Figure 2 .
Figure 2. Genome assembly of Gymnoscelis rufifasciata, ilGymRufi1.1: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 462,009,964 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 (22,195,239 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold ome lengths (15,602,950 and 8,767,853 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/ilGymRufi1.1/dataset/CAKMYF01/snail.

Figure 3 .
Figure 3. Genome assembly of Gymnoscelis rufifasciata, ilGymRufi1.1:GC coverage.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/ilGymRufi1.1/dataset/CAKMYF01/blob.

Figure 5 .
Figure 5. Genome assembly of Gymnoscelis rufifasciata, ilGymRufi1.1:Hi-C contact map.Hi-C contact map of the ilGymRufi1.1 assembly, visualised in HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this map is available here.

Figure 2
Figure 2/3/4/5 titles.These should be informative and tell the reader what you would like them to understand about the data; e.g., Fig 3. Little contamination was found in the final genome assembly.

Figure 4 .
Figure 4. has very little information and can easily be summarized as a sentence in the results.The same is true of Fig 5

Table 2 . Chromosomal pseudomolecules in the genome assembly of Gymnoscelis rufifasciata, ilGymRufi1.1. INSDC accession Chromosome Size (Mb) GC%
(operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.

Table 3 . Software tools used.
The genome sequence is released openly for reuse.The G. rufifasciata 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.The genome will be annotated and presented through the Ensembl pipeline at the European Bioinformatics Institute.Raw data and assembly accession identifiers are reported in Table1.
"A double brooded species, adults are first on the wing in the UK from March to May," is strange in grammar, please check it."Gymnoscelis rufifasciata is common across western and central Europe, and while it has long been common in southern England, observations in northern England and Scotland have increased dramatically since the year 2000."What means "observation"?

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

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.
https://doi.org/10.21956/wellcomeopenres.19690.r62472© 2023 North H.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.