The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792)
Douglas Boyes, Jonathan Davis, Sivasankaran Kuppusamy, Jeffrey Marcus, Carlos Lopez-Vaamonde
TL;DR
This paper reports the genome sequence of the Sandy Carpet moth, including a detailed assembly and gene annotation.
Contribution
The study provides a high-quality genome assembly and gene annotation for Perizoma flavofasciatum.
Findings
The genome assembly is 369.30 megabases long with 99.88% scaffolded into 30 chromosomal pseudomolecules.
The mitochondrial genome is 16.61 kilobases in length.
Gene annotation identified 11,915 protein-coding genes.
Abstract
We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 1
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Figure 4
Figure 5| Project information | |||
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| Perizoma flavofasciatum (sandy carpet) | ||
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| PRJEB63430 | ||
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| SAMEA7701445 | ||
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| 934819 | ||
| Specimen information | |||
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| ilPerFlao1 | SAMEA7701609 | Whole organism |
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| ilPerFlao2 | SAMEA112360821 | thorax |
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| ilPerFlao2 | SAMEA112360822 | abdomen |
| Sequencing information | |||
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| ERR11606315 | 6.07e+08 | 91.65 |
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| ERR11593799 | 2.00e+06 | 25.84 |
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| ERR11837494 | 7.68e+07 | 11.59 |
| Genome assembly | ||
|---|---|---|
| Assembly name | ilPerFlao1.1 | |
| Assembly accession | GCA_958496245.1 | |
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| Span (Mb) | 369.30 | |
| Number of contigs | 43 | |
| Number of scaffolds | 39 | |
| Longest scaffold (Mb) | 20.74 | |
| Assembly metrics
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| Contig N50 length (Mb) | 13.4 |
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| Scaffold N50 length (Mb) | 13.4 |
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| Consensus quality (QV) | 65.5 |
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| Primary: 88.65%; alternate:
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| BUSCO v5.4.3 lineage:
| C:98.2%[S:97.8%,D:0.4%],
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| Percentage of assembly mapped
| 99.88% |
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| Sex chromosomes | Z |
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| Organelles | Mitochondrial genome: 16.61
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| Genome annotation of assembly GCA_958496245.1 at Ensembl | ||
| Number of protein-coding genes | 11,915 | |
| Number of non-coding genes | 1,605 | |
| Number of gene transcripts | 22,268 | |
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| 1 | 20.74 | 36.5 | |
| 2 | 15.81 | 37.0 | |
| 3 | 15.75 | 37.0 | |
| 4 | 15.46 | 37.0 | |
| 5 | 15.35 | 36.5 | |
| 6 | 14.89 | 37.0 | |
| 7 | 14.63 | 36.5 | |
| 8 | 13.98 | 37.0 | |
| 9 | 13.86 | 37.0 | |
| 10 | 13.83 | 36.5 | |
| 11 | 13.42 | 37.0 | |
| 12 | 13.42 | 37.0 | |
| 13 | 12.96 | 37.0 | |
| 14 | 12.9 | 36.5 | |
| 15 | 12.72 | 37.0 | |
| 16 | 12.32 | 37.0 | |
| 17 | 12.15 | 37.0 | |
| 18 | 11.99 | 37.0 | |
| 19 | 11.94 | 37.0 | |
| 20 | 11.24 | 36.5 | |
| 21 | 11.2 | 37.5 | |
| 22 | 9.54 | 37.0 | |
| 23 | 9.2 | 36.5 | |
| 24 | 9.06 | 37.0 | |
| 25 | 8.06 | 36.5 | |
| 26 | 6.7 | 37.0 | |
| 27 | 6.17 | 37.5 | |
| 28 | 6.03 | 39.0 | |
| 29 | 5.97 | 38.0 | |
| Z | 17.6 | 37.0 | |
| MT | 0.02 | 19.5 |
| Software tool | Version | Source |
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| BEDTools | 2.30.0 |
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| BLAST | 2.14.0 |
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| BlobToolKit | 4.3.7 |
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| BUSCO | 5.4.3 and 5.5.0 |
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| bwa-mem2 | 2.2.1 |
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| Cooler | 0.8.11 |
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| DIAMOND | 2.1.8 |
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| fasta_windows | 0.2.4 |
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| FastK | 427104ea91c78c3b8b8b49f1a
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| Gfastats | 1.3.6 |
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| GoaT CLI | 0.2.5 |
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| Hifiasm | 0.19.8-r587 |
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| HiGlass | 44086069ee7d4d3f6f3f001256
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| Merqury.FK | d00d98157618f4e8d1a919002
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| MitoHiFi | 3 |
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| MultiQC | 1.14, 1.17, and 1.18 |
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| NCBI Datasets | 15.12.0 |
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| Nextflow | 23.04.0-5857 |
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| PretextView | 0.2.5 |
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| purge_dups | 1.2.5 |
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| samtools | 1.16.1, 1.17, and 1.18 |
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| sanger-tol/ascc | - |
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| sanger-tol/blobtoolkit | 0.6.0 |
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| Seqtk | 1.3 |
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| Singularity | 3.9.0 |
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| TreeVal | 1.0.0 |
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| YaHS | 1.2a.2 |
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- —Wellcome Trust
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Taxonomy
TopicsLepidoptera: Biology and Taxonomy · Insect Resistance and Genetics · Insect-Plant Interactions and Control
Species 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; Larentiinae; Perizoma; Perizoma flavofasciatum (Thunberg, 1792) (NCBI:txid934819)
Background
Perizoma flavofasciatum (family Geometridae), commonly known as the Sandy Carpet moth, is widely distributed across Europe and extends into parts of Asia. Its range includes most European countries and stretches eastwards through the Palaearctic region to the Urals and the Altai Mountains ( GBIF Secretariat, 2023). This species inhabits various environments across its range, such as meadow valleys, floodplains, waterside areas, bushy meadows, and gardens. In mountainous regions like the Alps, it can be found at elevations up to 1,500 metres.
Perizoma flavofasciatum has a wingspan of 26–32 mm ( Kimber, 2025). The species is characterised by the sandy brown cross-lines on a white ground colour and the two interneural blotches connecting the median and subterminal fasciae at about halfway between costa and dorsum ( British Lepidoptera, 2025).
In the UK, it is fairly common across Britain, particularly in the south of England ( GBIF Secretariat, 2023) and is listed as “least concern” in the macro-moth status review ( Fox et al., 2019). The adult flies from dusk onwards in June and July ( Kimber, 2025), and inhabits woodland, commons, chalky ground and other dry areas. The larvae feed on the seed-pods of campions ( Silene spp.) ( Waring et al., 2017).
We present a chromosomal-level genome sequence for Perizoma flavofasciatum, based on a male specimen from Wytham Woods, Berkshire, United Kingdom ( Figure 1). This was sequenced as part of the Darwin Tree of Life project.
Photograph of the Perizoma flavofasciatum (ilPerFlao1) specimen used for genome sequencing.
Genome sequence report
The genome of Perizoma flavofasciatum ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating a total of 25.84 Gb (gigabases) from 2.00 million reads, providing an estimated 66-fold coverage. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data, which produced 91.65 Gb from 606.97 million reads. Specimen and sequencing details are summarised in Table 1.
Table 1.: Specimen and sequencing data for Perizoma flavofasciatum.
Assembly errors were corrected by manual curation, including three missing joins or mis-joins. The final assembly has a total length of 369.30 Mb in 39 sequence scaffolds, with three gaps. The scaffold N50 is 13.4 Mb ( Table 2).
Table 2.: Genome assembly data for Perizoma flavofasciatum, ilPerFlao1.1.
The snail plot in Figure 2 provides a summary of the assembly statistics, indicating the distribution of scaffold lengths and other assembly metrics. Figure 3 shows the distribution of scaffolds by GC proportion and coverage. Figure 4 presents a cumulative assembly plot, with separate curves representing different scaffold subsets assigned to various phyla, illustrating the completeness of the assembly.
Genome assembly of Perizoma flavofasciatum, ilPerFlao1.1: metrics.The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the whole genome sequence, and the main plot is divided into 1,000 bins around the circumference. The outermost blue tracks display the distribution of GC, AT, and N percentages across the bins. Scaffolds are arranged clockwise from longest to shortest and are depicted in dark grey. The longest scaffold is indicated by the red arc, and the deeper orange and pale orange arcs represent the N50 and N90 lengths. A light grey spiral at the centre shows the cumulative scaffold count on a logarithmic scale. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the lepidoptera_odb10 set is presented at the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilPerFlao1_1/dataset/ilPerFlao1_1/snail.
Genome assembly of Perizoma flavofasciatum, ilPerFlao1.1: BlobToolKit GC-coverage plot showing sequence coverage (vertical axis) and GC content (horizontal axis).The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilPerFlao1_1/dataset/ilPerFlao1_1/blob.
Genome assembly of Perizoma flavofasciatum ilPerFlao1.1: 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/ilPerFlao1_1/dataset/ilPerFlao1_1/cumulative.
Most of the assembly sequence (99.88%) was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome. These chromosome-level scaffolds, confirmed by the Hi-C data, are named in order of size ( Figure 5; Table 3). During manual curation the Z chromosome was identified based on synteny with Eulithis prunata (GCA_918843925.1) ( Boyes et al., 2023).
Genome assembly of Perizoma flavofasciatum ilPerFlao1.1: Hi-C contact map of the ilPerFlao1.1 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=KlJLbAflRRWP4E1ra_QFAQ.
Table 3.: Chromosomal pseudomolecules in the genome assembly of Perizoma flavofasciatum, ilPerFlao1.
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, and as a separate fasta file.
The final assembly has a Quality Value (QV) of 65.5. The k-mer completeness value for the primary assembly was estimated as 88.65%, for the alternate haplotype was 82.01%, and of the combined assemblies was 99.57%. BUSCO (v5.4.3) analysis using the lepidoptera_odb10 reference set ( n = 5,286) indicated a completeness score of 98.2% (single = 97.8%, duplicated = 0.4%). The assembly achieves the EBP reference standard of 6.7.65. Other quality metrics are given in Table 2.
Genome annotation report
The Perizoma flavofasciatum genome assembly (GCA_958496245.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 22,268 transcribed mRNAs from 11,915 protein-coding and 1,605 non-coding genes ( Table 2; https://rapid.ensembl.org/Perizoma_flavofasciatum_GCA_958496245.1/Info/Index). The average transcript length is 14,574.44. There are 1.65 coding transcripts per gene and 7.73 exons per transcript.
Methods
Sample acquisition and DNA barcoding
An adult male specimen of Perizoma flavofasciatum (specimen ID Ox000581, ToLID ilPerFlao1) was collected from Wytham Woods, Berkshire, United Kingdom (latitude 51.77, longitude –1.34) on 2020-07-05, using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and on dry ice.
The specimen used for Hi-C and RNA sequencing (specimen ID SAN00002560, ToLID ilPerFlao2) was collected from Little Sparta, Dunsyre, Pentland Hills, South Lanarkshire, Scotland (latitude 55.72, longitude –3.50) on 2022-06-17. The specimen was collected and identified by Jo Davis (independent researcher).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023b). The ilPerFlao1 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the whole organism was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a). HMW DNA was extracted using the Automated MagAttract v1 protocol ( Sheerin et al., 2023). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Todorovic et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation, using AMPure PB beads to eliminate shorter fragments and concentrate the DNA ( Strickland et al., 2023). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. The fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from abdomen tissue of ilPerFlao2 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.
Hi-C preparation
Thorax tissue of the ilPerFlao2 sample was processed at the WSI Scientific Operations core, using the Arima-HiC v2 kit. Tissue (stored at –80 °C) was fixed, and the DNA crosslinked using a TC buffer with 22% formaldehyde. After crosslinking, the tissue was homogenised using the Diagnocine Power Masher-II and BioMasher-II tubes and pestles. Following the kit manufacturer's instructions, crosslinked DNA was digested using a restriction enzyme master mix. The 5’-overhangs were then filled in and labelled with biotinylated nucleotides and proximally ligated. An overnight incubation was carried out for enzymes to digest remaining proteins and for crosslinks to reverse. A clean up was performed with SPRIselect beads prior to library preparation.
Library preparation and sequencing
** PacBio HiFi **
Libraries were prepared using the PacBio Express Template Preparation Kit v2.0 (Pacific Biosciences, California, USA) as per the manufacturer's instructions. The kit includes the reagents required for removal of single-strand overhangs, DNA damage repair, end repair/A-tailing, adapter ligation, and nuclease treatment. Library preparation also included a library purification step using AMPure PB beads (Pacific Biosciences, California, USA) and size selection step to remove templates shorter than 3 kb using AMPure PB modified SPRI. DNA concentration was quantified using the Qubit Fluorometer v2.0 (Thermo Fisher Scientific) and Qubit HS Assay Kit and the final library fragment size analysis was carried out using the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies).
Samples were sequenced using the Sequel IIe system (Pacific Biosciences, California, USA). The concentration of the library loaded onto the Sequel IIe was in the range 40–135 pM. The SMRT link software, a PacBio web-based end-to-end workflow manager, was used to set-up and monitor the run, as well as perform primary and secondary analysis of the data upon completion.
** Hi-C data **
For Hi-C library preparation, DNA was fragmented to a size of 400 to 600 bp using a Covaris E220 sonicator. The DNA was then enriched, barcoded, and amplified using the NEBNext Ultra II DNA Library Prep Kit following manufacturers’ instructions. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on an Illumina NovaSeq 6000 instrument.
** RNA **
Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit, following the manufacturer’s instructions. RNA sequencing was performed on the Illumina NovaSeq 6000 instrument.
Genome assembly, curation and evaluation
** Assembly **
The HiFi reads were first assembled using Hifiasm ( Cheng et al., 2021) with the --primary option. Haplotypic duplications were identified and removed using purge_dups ( Guan et al., 2020). The Hi-C reads were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). The contigs were further scaffolded using the provided Hi-C data ( Rao et al., 2014) in YaHS ( Zhou et al., 2023) using the --break option for handling potential misassemblies. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al., 2022), BUSCO ( Manni et al., 2021) and MERQURY.FK ( Rhie et al., 2020).
The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), 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.
** Assembly curation **
The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants (ASCC) pipeline (article in preparation). Flat files and maps used in curation were generated in TreeVal ( Pointon et al., 2023). Manual curation was primarily conducted using PretextView ( Harry, 2022), with additional insights provided by JBrowse2 ( Diesh et al., 2023) and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were corrected, and duplicate sequences were tagged and removed. The sex chromosome was identified by synteny analysis. The curation process is documented at https://gitlab.com/wtsi-grit/rapid-curation (article in preparation).
** Assembly quality assessment **
The Merqury.FK tool ( Rhie et al., 2020) was used to evaluate k-mer completeness and assembly quality for the primary and alternate haplotypes using the k-mer databases ( k = 31) that were pre-computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
A Hi-C contact map was produced for the final, public version of the assembly. The Hi-C reads were aligned using bwa-mem2 ( Vasimuddin et al., 2019) and the alignment files were combined using SAMtools ( Danecek et al., 2021). The Hi-C alignments were converted into a contact map using BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020). The contact map is visualised in HiGlass ( Kerpedjiev et al., 2018).
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.
Genome annotation
The Ensembl Genebuild annotation system ( Aken et al., 2016) was used to generate annotation for the Perizoma flavofasciatum assembly (GCA_958496245.1) in Ensembl Rapid Release at the EBI. 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.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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- 2Aken BL Ayling S Barrell D : The Ensembl gene annotation system. Database (Oxford). 2016;2016: baw 093. 10.1093/database/baw 093 27337980 PMC 4919035 · doi ↗ · pubmed ↗
- 3Allio R Schomaker-Bastos A Romiguier J : Mito Finder: 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 PMC 7497042 · doi ↗ · pubmed ↗
- 4Boyes D Holland PWH , University of Oxford and Wytham Woods Genome Acquisition Lab, : The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758) [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Res. 2023;8:185. 10.12688/wellcomeopenres.19371.1 38404637 PMC 10891429 · doi ↗ · pubmed ↗
- 5British Lepidoptera: Perizoma flavofasciata (Sandy Carpet).2025; [Accessed 13 January 2025]. Reference Source
- 6Challis R Richards E Rajan J : Blob Tool Kit – interactive quality assessment of genome assemblies. G 3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g 3.119.400908 32071071 PMC 7144090 · doi ↗ · pubmed ↗
- 7Cheng 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/s 41592-020-01056-5 33526886 PMC 7961889 · doi ↗ · pubmed ↗
- 8Danecek P Bonfield JK Liddle J : Twelve years of SA Mtools and BC Ftools. Giga Science. 2021;10(2): giab 008. 10.1093/gigascience/giab 008 33590861 PMC 7931819 · doi ↗ · pubmed ↗