The genome sequence of the Water Carpet, Lampropteryx suffumata (Denis & Schiffermiiller, 1775).

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Learn more: PMC Disclaimer | PMC Copyright Notice Wellcome Open Res . 2026 Mar 9;8:304. Originally published 2023 Jul 12. [Version 2] doi: 10.12688/wellcomeopenres.19654.2 Other versions PMC13080333.1; 2023 Jul 12 PMC13080333.2; 2026 Mar 9 Search in PMC Search in PubMed View in NLM Catalog Add to search The genome sequence of the Water Carpet, Lampropteryx suffumata (Denis & Schiffermiiller, 1775) Douglas Boyes Douglas Boyes 1 UK Centre for Ecology & Hydrology, Wallingford, England, UK Investigation, Resources Find articles by Douglas Boyes 1 , Peter WH Holland Peter WH Holland 2 University of Oxford, Oxford, England, UK Writing – Original Draft Preparation, Writing – Review & Editing Find articles by Peter WH Holland 2 ; University of Oxford and Wytham Woods 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 Consortium a Author information Article notes Copyright and License information 1 UK Centre for Ecology & Hydrology, Wallingford, England, UK 2 University of Oxford, Oxford, England, UK a Email: mark.blaxter@sanger.ac.uk + Deceased author No competing interests were disclosed. Roles Douglas Boyes : Investigation, Resources Peter WH Holland : Writing – Original Draft Preparation, Writing – Review & Editing Accepted 2026 Feb 7; Collection date 2023. Copyright: © 2026 Boyes D et al. 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. PMC Copyright notice PMCID: PMC13080333  PMID: 41994310 Version Changes Revised. Amendments from Version 1 Version 2 of this data note includes a full table giving the assembly metrics against the Earth BioGenome Project benchmarks (Table 3). We have corrected the Merqury.FK results using a new version of the software. We have added a sentence to the abstract to state that this assembly was generated as part of the Darwin Tree of Life Project. Abstract We present a genome assembly from an individual male Lampropteryx suffumata (the Water Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 581.6 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 16.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,663 protein coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland. Keywords: Lampropteryx suffumata, Water Carpet, genome sequence, chromosomal, Lepidoptera Species taxonomy Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Geometroidea; Geometridae; Larentiinae; Lampropteryx ; Lampropteryx suffumata (Denis & Schiffermiiller, 1775) (NCBI:txid934945). Background Many species of insect are found widely across the Palaearctic realm from Europe to Asia, but relatively few have distributions that also extend to North America. Some exceptions include highly migratory species and those transported by human activity. A land connection existed until around five million years ago, the Bering land bridge, and until the land connection was lost there was some dispersal of species in each direction ( Gladenkov et al. , 2002 ; Jiang et al. , 2019 ). The Water Carpet Lampropteryx suffumata is a moth in the family Geometridae now known to exist on both sides of the Bering Strait. In Eurasia, the species is found commonly in northern and central Europe with the largest numbers of records from Britain, Scandinavia and Austria; there are scattered records ranging from Ireland and France in the west across to the far east of Russia, including Khabarovsk Krai and the Kamchatka peninsula, and on the Japanese island of Hokkaido ( Beljaev & Vasilenko, 2002 ; Beljaev et al. , 2022 ). In 2000 eight specimens of L. suffumata were recorded from Alaska, and in 2008 several Canadian specimens in museum collections were retrospectively identified as L. suffumata by DNA barcoding, including a historical specimen dating from 1919 ( Choi, 2000 ; Dewaard et al. , 2008 ). There is no suggestion that these North American individuals were accidentally introduced. Hence, the longitudinal range of L. suffumata extends from the Dingle Peninsula, Ireland, eastward across Eurasia and the Bering Strait to reach Alberta, Canada. Like most ‘carpet’ moths, named for their resemblance to the intricate patterns on woven carpets, the Water Carpet rests with its wings flat against the surface in a delta shape. The forewings are silvery-grey with a deeply indented brown cross-band outlined in white. In Britain and Ireland, the moth is on the wing from March to May, with the emergence time having moved earlier in the year since the 1970s ( Randle et al. , 2019 ). The species is most commonly encountered in damp woodland, moorland and fens, where the larvae feed on cleavers ( Galium aparine ) and other Galium species; the pupal stage overwinters ( South, 1961 ; Waring et al. , 2017 ). The complete genome sequence of Lampropteryx suffumata was determined as part of the Darwin Tree of Life project. The assembled genome will facilitate studies into the biogeography and population genetics of this widespread species and contribute to the growing set of resources for studying insect ecology and evolution. This assembly is the only publicly available genome for the genus Lampropteryx as of February 2026, based on data obtained via NCBI Datasets ( O’Leary et al. , 2024 ). Genome sequence report The genome was sequenced from one male Lampropteryx suffumata ( Figure 1 ) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.34). A total of 39-fold coverage in Pacific Biosciences single-molecule HiFi long was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 31 missing joins or mis-joins and removed 16 haplotypic duplications, reducing the assembly length by 1.99 % and the scaffold number by 11.86%, and increasing the scaffold N50 by 1.22%. Figure 1. Photograph of the Lampropteryx suffumata (ilLamSuff1) specimen used for genome sequencing. Open in a new tab The final assembly has a total length of 581.6 Mb in 51 sequence scaffolds with a scaffold N50 of 20.0 Mb ( Table 1 ). Most (99.81%) 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 ). The Z chromosome was identified based on synteny with Eulithis prunata (GCA_918843925.1) ( Boyes & Holland, 2023 ). 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 Lampropteryx suffumata , ilLamSuff1.1. Project accession data Assembly identifier ilLamSuff1.1 Species Lampropteryx suffumata Specimen ilLamSuff1 NCBI taxonomy ID 934945 BioProject PRJEB58348 BioSample ID SAMEA10107026 Isolate information ilLamSuff1, male: thorax (DNA sequencing), head (Hi-C scaffolding), abdomen (RNA sequencing) Raw data accessions PacificBiosciences SEQUEL II ERR10677858 Hi-C Illumina ERR10684086 PolyA RNA-Seq Illumina ERR11242515 Genome assembly Assembly accession GCA_948098915.1 Accession of alternate haplotype GCA_948098925.1 Span (Mb) 581.6 Number of contigs 122 Contig N50 length (Mb) 9.5 Number of scaffolds 51 Scaffold N50 length (Mb) 20.0 Longest scaffold (Mb) 29.7 Genome annotation Number of protein-coding genes 18,663 Number of gene transcripts 18,828 Open in a new tab Figure 2. Genome assembly of Lampropteryx suffumata , ilLamSuff1.1: metrics. Open in a new tab 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 581,655,136 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 (29,738,398 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (19,956,036 and 13,321,282 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/Lampropteryxsuffumata/dataset/CANUEU01/snail . Figure 5. Genome assembly of Lampropteryx suffumata , ilLamSuff1.1: Hi-C contact map of the ilLamSuff1.1 assembly, visualised using HiGlass. Open in a new tab 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=TwZBJG1cSRCC_If8XAVIzA . Table 2. Chromosomal pseudomolecules in the genome assembly of Lampropteryx suffumata , ilLamSuff1. INSDC accession Chromosome Length (Mb) GC% OX402545.1 1 22.97 36.5 OX402546.1 2 21.6 36.5 OX402547.1 3 21.41 36.0 OX402548.1 4 21.33 36.5 OX402549.1 5 21.26 36.5 OX402550.1 6 21.19 36.0 OX402551.1 7 20.83 36.0 OX402552.1 8 20.76 36.5 OX402553.1 9 20.58 36.0 OX402554.1 10 20.5 36.5 OX402555.1 11 20.31 36.5 OX402556.1 12 20.08 36.5 OX402557.1 13 19.96 36.0 OX402558.1 14 19.72 36.0 OX402559.1 15 19.39 36.0 OX402560.1 16 19.15 36.5 OX402561.1 17 19.13 36.0 OX402562.1 18 19.06 36.5 OX402563.1 19 19.04 36.5 OX402564.1 20 18.56 36.0 OX402565.1 21 18.43 36.5 OX402566.1 22 17.08 36.5 OX402567.1 23 16.89 36.0 OX402568.1 24 16.04 36.0 OX402569.1 25 14.27 37.0 OX402570.1 26 13.32 36.5 OX402571.1 27 13.21 36.0 OX402572.1 28 12.39 37.0 OX402573.1 29 11.81 36.5 OX402574.1 30 10.39 38.0 OX402544.1 Z 29.74 36.0 OX402575.1 MT 0.02 18.5 Open in a new tab Figure 3. Genome assembly of Lampropteryx suffumata , ilLamSuff1.1: BlobToolKit GC-coverage plot. Open in a new tab 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/Lampropteryxsuffumata/dataset/CANUEU01/blob . Figure 4. Genome assembly of Lampropteryx suffumata , ilLamSuff1.1: BlobToolKit cumulative sequence plot. Open in a new tab 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/Lampropteryxsuffumata/dataset/CANUEU01/cumulative . The combined primary and alternate assemblies achieve an estimated QV of 65.2. The k -mer completeness is 77.22% for the primary assembly, 74.64% for the alternate haplotype, and 99.31% for the combined assemblies. The primary assembly has a BUSCO v5.3.2 completeness of 98.2% (single = 97.7%, duplicated = 0.5%), using the lepidoptera_odb10 reference set ( n = 5,286). Table 3 lists the assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024 . The EBP metric, calculated for the primary assembly, is 6.C.Q64 , meeting the recommended reference standard. Table 3. Earth Biogenome Project summary metrics for the Lampropteryx suffumata assembly. Measure Value Benchmark EBP summary (primary) 6.C.Q64 6.C.Q40 Contig N50 length 9.51 Mb ≥ 1 Mb Scaffold N50 length 19.96 Mb = chromosome N50 Consensus quality (QV) Primary: 64.7; alternate: 65.4; combined: 65.2 ≥ 40 k -mer completeness Primary: 77.22%; alternate: 74.64%; combined: 99.31% ≥ 95% BUSCO C:98.2%[S:97.7%,D:0.5%], F:0.4%,M:1.4%,n:5,286 S > 90%; D < 5% Percentage of assembly assigned to chromosomes 99.82% ≥ 90% Open in a new tab Notes: EBP summary uses log10(Contig N50); chromosome-level (C) or log10(Scaffold N50); Q (Merqury QV). BUSCO: C=complete; S=single-copy; D=duplicated; F=fragmented; M=missing; n=orthologues. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Lampropteryx suffumata/dataset/CANUEU01/busco . Genome annotation report The Lampropteryx suffumata genome assembly (GCA_948098915.1) was annotated by Ensembl at the European Bioinformatics Institute (EBI). This annotation includes 18 828 transcribed mRNAs from 18 663 protein-coding genes. The average transcript length is 8 213.15 bp, with an average of 5.39 exons per transcript. Further details of this annotation are available from the Ensembl annotation page . Methods Sample acquisition and nucleic acid extraction The specimen used for genome sequencing was a male Lampropteryx suffumata (specimen ID Ox001102 , ilLamSuff1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude –1.34) on 2021-03-31 using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford), and was snap-frozen on dry ice. The specimen was prepared for DNA extraction at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilLamSuff1 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. DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer’s instructions. RNA was extracted from abdomen tissue of ilLamSuff1 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. Protocols for high molecular weight (HMW) DNA extraction developed at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory are available on protocols.io ( Howard et al. , 2025 ). 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 tissue of ilLamSuff1 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. , 2022 ), which runs MitoFinder ( Allio et al. , 2020 ) 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.FK ( Rhie et al. , 2020 ). The genome was analysed within the BlobToolKit environment ( Challis et al. , 2020 ) and BUSCO scores ( Manni et al. , 2021 ) were calculated. Table 4 contains a list of relevant software tool versions and sources. Table 4. Software tools: versions and sources. Software tool Version Source BlobToolKit 4.1.5 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 0.2.5 https://github.com/wtsi-hpag/PretextView purge_dups 1.2.3 https://github.com/dfguan/purge_dups YaHS 1.2a https://github.com/c-zhou/yahs Open in a new tab Genome annotation The BRAKER2 pipeline ( Brůna et al. , 2021 ) was used in the default protein mode to generate annotation for the Lampropteryx suffumata assembly (GCA_948098915.1) in Ensembl Rapid Release. Wellcome Sanger Institute – Legal and Governance The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’ , which can be found in full on the Darwin Tree of Life website here . By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project. Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material • Legality of collection, transfer and use (national and international) Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators. Data availability European Nucleotide Archive: Lampropteryx suffumata (water carpet). Accession number PRJEB58348; https://identifiers.org/ena.embl/PRJEB58348 . ( Wellcome Sanger Institute, 2023 ) The genome sequence is released openly for reuse. The Lampropteryx suffumata 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 . Production code used in genome assembly at the WSI Tree of Life is available at https://github.com/sanger-tol . Table 5 lists software versions used in this study. Author information Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4789928 . 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 . Funding Statement 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. [version 2; peer review: 2 approved, 1 approved with reservations] References 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 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. 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Bioinformatics. 2023;39(1): btac808. 10.1093/bioinformatics/btac808 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Wellcome Open Res. 2026 Apr 14. doi: 10.21956/wellcomeopenres.28659.r151917 Reviewer response for version 2 Wai Lok So Wai Lok So 1 The Hang Seng University of Hong Kong (Ringgold ID: 272025), Hong Kong, Hong Kong Referee Find articles by Wai Lok So 1 Author information Copyright and License information 1 The Hang Seng University of Hong Kong (Ringgold ID: 272025), Hong Kong, Hong Kong Competing interests: No competing interests were disclosed. Roles Wai Lok So : Referee Copyright: © 2026 So WL 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. PMC Copyright notice The manuscript presents a high-quality genome assembly of the moth, Lampropteryx suffumata, as a part of the Darwin Tree of Life initiative. The assembly methods are technically sound with excellent assembly scores. The authors have made sufficient amendments and improvements regarding the comments provided by the earlier reviewers. The resulting resource would be beneficial to future lepidopteran ecological and evolutionary studies. I have no major concerns with the manuscript. 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: evolution, genomics, arthropods, myriapods 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. Wellcome Open Res. 2024 Jul 4. doi: 10.21956/wellcomeopenres.21771.r77250 Reviewer response for version 1 Xiaolei Huang Xiaolei Huang 1 Fujian Agriculture and Forestry University, Fuzhou, Fujian, China Referee Find articles by Xiaolei Huang 1 Author information Copyright and License information 1 Fujian Agriculture and Forestry University, Fuzhou, Fujian, China Competing interests: No competing interests were disclosed. Roles Xiaolei Huang : Referee Copyright: © 2024 Huang X 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. PMC Copyright notice The article reports a genome assembly of the carpet moth Lampropteryx suffumata, which is a widespread species with longitudinal range across the Eurasia and the North America. The genome sequence data will facilitate phylogenetics, biogeography and population genetic studies. As part of the Darwin Tree of Life project, this Data Note article follows a standardized format, and presents sufficient details of research materials and analysis procedures. I think the article is well prepared. My only minor suggestion is maybe the authors can provide more details such as parameter configurations of specific tools using in some key analyses, if the authors also think this is necessary. 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: insect ecology and evolution 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. Wellcome Open Res. 2024 Jun 6. doi: 10.21956/wellcomeopenres.21771.r83936 Reviewer response for version 1 Christopher B Cunningham Christopher B Cunningham 1 University of Georgia, Athens, Georgia, USA Referee Find articles by Christopher B Cunningham 1 Author information Copyright and License information 1 University of Georgia, Athens, Georgia, USA Competing interests: No competing interests were disclosed. Roles Christopher B Cunningham : Referee Copyright: © 2024 Cunningham CB 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. PMC Copyright notice The project continues to produce quality resources for the insect genomics community. The methods are sound and relatively well documented. The article needs a few more details to be reasonably reproducible. Abstract. There is no justification within the abstract, just results. At least a sentence that this was part of a large survey of insects is needed. And one sentence for its possible value. Keywords. Not present. Background. There is little true motivation for this study in the introduction. Nothing wrong is said, but the reader has little idea why the work was done. Almost all the details of its life history are irrelevant to the reader. 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. has very little information and can easily be summarized as a sentence in the results. The same is true of Fig 5 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? A reasonable, likely slightly high, number of genes is predicted. However, the reader has very little understanding of how these were evaluated beyond their initial generation. What QC beyond an automated annotation was done? One annotation run with default parameters should come with a strong disclaimer that any further work on specific gene families requires QC on the part of the user because the current annotation is a guide only. What is the BUSCO percentage of the predicted gene set? That is an absolute minimum for a reader to be able to assess the minimum quality of the annotation. How many orthogroups with other insects, etc? Table 3 is of little to no value and contains much duplicated information. Just add the version numbers of software used in line at the appropriate places in the methods section. Is the Ethics statement needed? It just says the provider of the sample should meet some agreed upon standard, but does not actually say that they did in this case. Either drop the statement or actually say the standard was met for this sample. This is not a paper about the standards of collection. 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. 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? Yes Are the protocols appropriate and is the work technically sound? Yes Reviewer Expertise: Behavior, Reproduction, Genetics, Genomics, Epigenetics, 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, however I have significant reservations, as outlined above. Wellcome Open Res. 2026 Feb 5. Tree of Life Team Sanger Tree of Life Team Sanger 1 Wellcome Trust Sanger Institute, UK Find articles by Tree of Life Team Sanger 1 Author information Copyright and License information 1 Wellcome Trust Sanger Institute, UK Competing interests: No competing interests were disclosed. PMC Copyright notice Thank you for reviewing this data note. Several of the comments raise broader points about the scope and purpose of data notes. While we have addressed points where clarification was appropriate, the manuscript intentionally follows the established data note format, which is designed to describe the generation, structure and quality of a dataset rather than to present biological interpretation or comparative analyses. Abstract: We have added a sentence stating that this genome assembly was generated as part of a large-scale eukaryote sequencing effort within the Darwin Tree of Life project. Keywords: These are provided in article metadata and appear in the PDF version. This is determined by the journal layout rather than the manuscript content. Background and rationale: The Background section provides a concise rationale for sequencing this species in the context of the Darwin Tree of Life programme. This programme aims to generate high-quality reference genomes across taxonomic breadth rather than to address a single hypothesis for each species. We have reviewed available sequence data and added a sentence to the background, which supports the importance of the genome presented here. Figures 2–5: These figures present standard quality assessments used across genome data notes, allowing consistency and comparability across studies. Their purpose is to summarise assembly properties and quality metrics rather than to test hypotheses. Parameter settings and defaults: All analyses were run using standard pipelines with default parameters unless otherwise stated. We have added a link to the GitHub repository for Tree of Life production code. Genome annotation and quality control: Genome annotation was produced by an external annotation team using established automated workflows. We link to these resources to ensure accessibility for users, but the annotation was not generated or curated by the authors of this manuscript. Table 3: (Now Table 4.) is retained as a consolidated reference for software tools and repositories used. Listing version numbers inline throughout the Methods would substantially reduce readability. We note that reviewer preferences on this point vary, and the current presentation aligns with other published data notes. Ethics statement: The Ethics statement is a mandatory requirement for our institute and reflects compliance with agreed standards for sample collection. Associated Data This section collects any data citations, data availability statements, or supplementary materials included in this article. Data Citations Wellcome Sanger Institute: The genome sequence of the Water Carpet , Lampropteryx suffumata (Denis & Schiffermiiller, 1775). European Nucleotide Archive.[dataset], accession number PRJEB58348,2023. Data Availability Statement European Nucleotide Archive: Lampropteryx suffumata (water carpet). Accession number PRJEB58348; https://identifiers.org/ena.embl/PRJEB58348 . ( Wellcome Sanger Institute, 2023 ) The genome sequence is released openly for reuse. The Lampropteryx suffumata 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 . Production code used in genome assembly at the WSI Tree of Life is available at https://github.com/sanger-tol . Table 5 lists software versions used in this study. Author information Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4789928 . 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 . 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