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

10.12688/wellcomeopenres.19298.2
Data Note
Articles
The genome sequence of the Streak, Chesias legatella (Denis & Schiffermüller, 1775)
[version 2; peer review: 2 approved, 1 approved with reservations]

Lees David Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-7580-8560
1
Natural History Museum Genome Acquisition Lab
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 Natural History Museum, London, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

3 9 2024
2023
8 20530 8 2024
Copyright: © 2024 Lees 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 Chesias legatella (the Streak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 310.3 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 20.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,520 protein-coding genes.

Chesias legatella
the Streak
genome sequence
chromosomal
Lepidoptera
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. Revised Amendments from Version 1

Changes have been made to the text in response to reviewers' comments.  We have added information about genome annotation of Chesias legatella. We now link to new annotation data from Ensembl at the European Bioinformatics Institute for the genome assembly reported in this data note. We attempted to improve the appearance of the specimen photograph of the sampled moth. The software Pretext was corrected to PretextView.
==== Body
pmcSpecies taxonomy

Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Larentiinae; Chesias; Chesias legatella (Denis & Schiffermüller, 1775) (NCBI:txid934925).

Background

The Streak, Chesias legatella, is a medium sized geometrid moth, dark greyish brown with a prominent creamish-white streak towards the apex of the forewing and an elliptic dark shape in the discal area with another whitish-cream dash inside, which flies late in the temperate season, usually September to early November in the UK ( Randle et al., 2019), overwintering as an egg. At rest it has a rather unusual posture for a looper moth, sometimes rolling its wings partially around a twig.

The Streak is a species of open woodland and heathland in the UK, especially on sandy substrates, feeding on Broom ( Cytisus scoparius L.) ( Wall, 1975), or occasionally Tree Lupin ( Lupinus arboreus) ( Wall, 1975; Waring et al., 2017).

C. legatella is generally common and widespread in the western Palaearctic only, from southern Scandinavia to the northern Mediterranean; but has relatively few records for eastern Europe ( GBIF Secretariat, 2022). It is widespread in the UK and eastern Ireland ( NBN Atlas Partnership, 2021), but the distribution is patchy, and it is vulnerable, with evidence for a significant decline since 1970 ( Conrad et al., 2006) that has affected its distribution ( Randle et al., 2019).

There is a single DNA barcode cluster on BOLD, BOLD:AAF2574 (16 March 2023), which is 5.46% pairwise divergent to that of Chesias capriata Prout, 1904 from Italy (BOLD:AAW3724). C. legatella has six other known congeners including the Broom-tip C. rufata (Fabricius, 1775) and belongs to the larentiine tribe Chesiadini, an early diverging one within the subfamily Larentiinae (after Trichopterygini), based on a study of ten nuclear protein coding genes and COI ( Murillo-Ramos et al., 2019: Figure 3). The genus Chesias falls sister to the genus Aplocera Stephens, 1827 in the study of Õunap, Viidalepp and Truuverk (2016: Figure 2). The whole genome will be useful for more detailed evolutionary studies.

The species is of no economic concern, although it has been considered as a possible agent of biological control of Broom ( Syrett et al., 1999).

The genome of Chesias legatella 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 Chesias legatella, based on one specimen from Beinn Eighe National Nature Reserve, Scotland.

Genome sequence report

The genome was sequenced from one male Chesias legatella ( Figure 1) collected from Beinn Eighe National Nature Reserve, Scotland, UK (latitude 57.63, longitude –5.35). A total of 53-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 seven missing or mis-joins and removed two haplotypic duplications, reducing the scaffold number by 5.26%.

Figure 1. Photograph of the Chesias legatella (ilCheLega1) specimen used for genome sequencing.

The final assembly has a total length of 310.3 Mb in 36 sequence scaffolds with a scaffold N50 of 11.0 Mb ( Table 1). Most (99.95%) 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 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.

Table 1. Genome data for Chesias legatella, ilCheLega1.1.

Project accession data	
Assembly identifier	ilCheLega1.1	
Species	Chesias legatella	
Specimen	ilCheLega1	
NCBI taxonomy ID	934925	
BioProject	PRJEB55725	
BioSample ID	SAMEA14448143	
Isolate information	ilCheLega1, head and thorax (genome sequencing and Hi-C
scaffolding)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	65.8	≥ 50	
k-mer completeness	100%	≥ 95%	
BUSCO **	C:98.4%[S:98.0%,D:0.4%],
F:0.5%,M:1.2%,n:5,286	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	99.95%	≥ 95%	
Sex chromosomes	Z chromosome	localised homologous pairs	
Organelles	Mitochondrial genome assembled	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10168717	
Hi-C Illumina	ERR10149547	
Genome assembly	
Assembly accession	GCA_947359385.1	
Accession of alternate haplotype	GCA_947359375.1	
Span (Mb)	310.3	
Number of contigs	80	
Contig N50 length (Mb)	6.2	
Number of scaffolds	36	
Scaffold N50 length (Mb)	11.0	
Longest scaffold (Mb)	15.0	
Genome annotation	
Number of protein-coding genes	15,520	
Number of gene transcripts	15,717	
* 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 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/ilCheLega1.1/dataset/CANAHS01/busco.

Figure 2. Genome assembly of Chesias legatella, ilCheLega1.1: 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 310,278,188 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 (14,956,362 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (11,018,016 and 7,493,246 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/ilCheLega1.1/dataset/CANAHS01/snail.

Figure 3. Genome assembly of Chesias legatella, ilCheLega1.1: 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/ilCheLega1.1/dataset/CANAHS01/blob.

Figure 4. Genome assembly of Chesias legatella, ilCheLega1.1: 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/ilCheLega1.1/dataset/CANAHS01/cumulative.

Figure 5. Genome assembly of Chesias legatella, ilCheLega1.1: Hi-C contact map of the ilCheLega1.1 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=ZLBbPbLmQzijgU5VCAKOxg.

Table 2. Chromosomal pseudomolecules in the genome assembly of Chesias legatella, ilCheLega1.

INSDC accession	Chromosome	Size (Mb)	GC%	
OX375763.1	1	14.01	36.8	
OX375764.1	2	13.87	37.2	
OX375765.1	3	13.53	37.1	
OX375766.1	4	13.5	36.5	
OX375767.1	5	13.22	36.9	
OX375768.1	6	13.02	37	
OX375769.1	7	12.11	37	
OX375770.1	8	12.02	37.1	
OX375771.1	9	11.91	37	
OX375772.1	10	11.51	37.4	
OX375773.1	11	11.17	37.3	
OX375774.1	12	11.02	37.1	
OX375775.1	13	10.42	37.5	
OX375776.1	14	10.06	37.3	
OX375777.1	15	10.02	37.8	
OX375778.1	16	10.02	37.8	
OX375779.1	17	9.91	37.4	
OX375780.1	18	9.47	37.5	
OX375781.1	19	9.47	37.7	
OX375782.1	20	9.15	37.4	
OX375783.1	21	9.1	37.3	
OX375784.1	22	8.91	37.5	
OX375785.1	23	8.57	37.5	
OX375786.1	24	7.53	38	
OX375787.1	25	7.49	37.4	
OX375788.1	26	7.07	38.1	
OX375789.1	27	4.79	38	
OX375790.1	28	4.31	38.4	
OX375791.1	29	4.02	40.2	
OX375792.1	30	3.99	39.4	
OX375762.1	Z	14.96	37	
OX375793.1	MT	0.02	18	

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/934925.

The estimated Quality Value (QV) of the final assembly is 65.8 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 98.4% (single = 98.0%, duplicated = 0.4%), using the lepidoptera_odb10 reference set ( n = 5,286).

Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/934925.

Genome annotation report

The Chesias legatella genome assembly (GCA_947359385.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 15,717 transcribed mRNAs from 15,520 protein-coding genes ( Table 1; https://rapid.ensembl.org/Chesias_legatella_GCA_947359385.1/Info/Index).

Methods

Sample acquisition and nucleic acid extraction

A male Chesias legatella (specimen number NHMUK014543814, ToLID ilCheLega1) was collected from Beinn Eighe National Nature Reserve, Scotland, UK (latitude 57.63, longitude –5.35) on 10 September 2021. The specimen was collected by David Lees (Natural History Museum) using a light trap. The specimen was identified by the collector and preserved at –80°C.

The ilCheLega1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Head and thorax tissue of ilCheLega1 was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. DNA was extracted at the Wellcome Sanger Institute (WSI) Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer’s instructions.

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 Pacific Biosciences SEQUEL II (HiFi) instrument. Hi-C data were also generated from tissue of ilCheLega1 using the Arima v2 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 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 PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2022), which performed annotation using MitoFinder ( Allio et al., 2020). To evaluate the assembly, MerquryFK was used to estimate consensus quality (QV) scores and k-mer completeness ( Rhie et al., 2020). The genome was analysed and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated within the BlobToolKit environment ( Challis et al., 2020). Table 3 contains a list of 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	
YaHS	yahs-1.1.91eebc2	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 Chesias legatella assembly (GCA_947359385.1) in Ensembl Rapid Release at the EBI.

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: Chesias legatella. Accession number PRJEB55725; https://identifiers.org/ena.embl/PRJEB55725. ( Wellcome Sanger Institute, 2022)

The genome sequence is released openly for reuse. The Chesias legatella 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.4790042.

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.24720.r96944
Reviewer response for version 2
Lucek Kay 1Referee https://orcid.org/0000-0002-2253-2556

1 Department of Environmental Sciences, University of Neuchâtel, Neuchâtel,, Switzerland
5 9 2024 Copyright: © 2024 Lucek K
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 2recommendationapprove
I appreciate clarification concerning the annotation.

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

Partly

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:

Speciation, Genomics, Evolutionary Biology, Lepidoptera

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.24720.r96946
Reviewer response for version 2
Alqahtani Fahad 1Referee https://orcid.org/0000-0002-2498-4871

1 King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
5 9 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 2recommendationapprove
I am happy with the manuscript in its current form.

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.

10.21956/wellcomeopenres.21381.r71927
Reviewer response for version 1
Nomura Shota 1Referee https://orcid.org/0000-0002-6843-787X

1 Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan
1 3 2024 Copyright: © 2024 Nomura 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-with-reservations
This study performed the chromosome-level genome assembly of the Streak, Chesias legatella. Authors assembled the contigs using PacBio single-molecule HiFi long reads and scaffolded them using Hi-C data. As a result, the authors obtained 36 scaffolds with 11.0 Mb of N50 and 98.4% of BUSCO score. Among the assembly, 99.95% were assigned to 30 autosomes and the Z sex chromosomes, resulting in a chromosome-level genome assembly with very high completeness.

In this manuscript, the methods of analyses were appropriate and well explained. I note below a few minor questions.

1. Authors wrote “the whole genome will be useful for more detailed evolutionary studies”. How many species of the same genus or tribe have chromosome-level genome sequences been published? This information would be useful to readers who wants to perform evolutionary studies and would be better to be explained in the paragraph.

2. As well as other papers submitted to Wellcome open research, genome annotation analyses should be performed using BRAKER2 or others pipeline. Annotation information is very useful to readers who use the assembled genome sequences for other studies. Also, the statement in Data Availability section (“The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute”) should be modified.

3. How did authors distinguish Z sex chromosomes from autosomes? If authors obtained male and female reads, they can be distinguished based on differences in reads mapping between the sexes. Did the authors use such a method? In any case, it would be better to be explained the methods of distinguish them.

4. “Hi-C data” should be changed to “Hi-C library” in Sequencing paragraph in Method section.

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

Partly

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:

Evolutionary ecology, genomics, RNA-seq, insect, Carabidae, speciation, sexual selection

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.21381.r75002
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
26 2 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
This paper is about the genome sequence of the Streak, Chesias legatella (Denis & Schiffermüller, 1775), the authors report that they successful reconstructed the genome at the chromosomal-level for a male specimen of Chesias legatella. They utilized two sequencing technologies, Pacific Biosciences SEQUEL II and Hi-C Illumina, to assemble the genome, which is approximately 310.3 Mb in size. The completeness of the genome assembly was assessed with BUSCO analysis, which contains 98.4% of common genes were completely present.

However, minor comments should be addressed:

- The photo of the Streak, Chesias legatella in Figure 1 needs to be imporoved.

- The NCBI-BioSample (SAMEA14448143) entry should be updated to reflect that the specimen is male, as stated in the paper.

- It is recommended to mention the related species used for guiding the mitochondrial genome annotation with the Mitofinder tool in the methods section.

- The term "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.

10.21956/wellcomeopenres.21381.r71925
Reviewer response for version 1
Lucek Kay 1Referee https://orcid.org/0000-0002-2253-2556

1 Department of Environmental Sciences, University of Neuchâtel, Neuchâtel,, Switzerland
8 1 2024 Copyright: © 2024 Lucek K
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 genome sequence of Chesias legatella is providing great potential for future evolutionary studies. Importantly, the notion that this species could be used as an agent for biological control “probably without consequences” needs to be carefully assessed before such measures would be implemented.

Overall the standard pipelines for genome assembly of the Darwin Tree of Life project have been thoroughly implemented.

Although the data availability statement suggests that "available RNA-Seq data" will be used to annotate the genome, no information on how this dataset has been generated or information about its quality are provided.

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

Partly

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:

Speciation, Genomics, Evolutionary Biology, Lepidoptera

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.

Sanger Tree of Life Team Wellcome Trust Sanger Institute, UK

11 5 2024 Thank you for your comments on this data note.  We would like to clarify the statement in the Data availability section: "The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute." This is not intended to refer to RNA-Seq generated as part of the dataset presented here. We have not presented RNA data here, and the Ensembl Rapid Annotation pipeline uses RNA data from different sources. 

We have added Ensembl annotation to the new version of this article, which was provided via their BRAKER2 pipeline. This annotation is generated externally to the Wellcome Sanger Institute.

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
==== Refs
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
Brůna T Hoff KJ Lomsadze A : BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom Bioinform. 2021;3 (1 ): lqaa108. 10.1093/nargab/lqaa108 33575650
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 M 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
GBIF Secretariat: Chesias legatella (Denis & Schiffermüller) 1775. GBIF Backbone Taxonomy. Checklist dataset,2022; (Accessed: 16 March 2023). 10.15468/39omei
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
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
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
NBN Atlas Partnership: Chesias legatella ([Denis & Schiffermüller], 1775): Streak.NBN Atlas,2021. Reference Source
Õunap E Viidalepp J Truuverk A : Phylogeny of the subfamily Larentiinae (Lepidoptera: Geometridae): integrating molecular data and traditional classifications. Syst Entomol. 2016;41 (4 ):824–843. 10.1111/syen.12195
Randle Z Evans-Hill LJ Parsons MS : Atlas of Britain & Ireland’s larger moths.Newbury: NatureBureau,2019.
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
Syrett P Fowler SV Coombs EM : The potential for biological control of Scotch broom ( Cytisus scoparius) (Fabaceae) and related weedy species. Biocontrol News and Information. 1999;20 (1 ):17N–33N. Reference Source
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
Wall C : The biology of the British species of Chesias (Lepidoptera: Geometridae). Entomologist’s Gazette. 1975;26 :89–106.
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 Streak, Chesias legatella (Denis & Schiffermüller, 1775). European Nucleotide Archive.[dataset], accession number PRJEB55725,2022.
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
