The genome sequence of the Broken-barred Carpet, Electrophaes corylata (Thunberg, 1792)

We present a genome assembly from an individual male Electrophaes corylata (the Broken-barred Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 347.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,031 protein coding genes.


Background
The Broken-barred Carpet (Electrophaes corylata) is a small geometrid moth whose larvae feed on a variety of broadleafed tree species.It occurs in a range of habitats including woodlands, gardens and hedgerows (Henwood et al., 2020;Waring et al., 2017).
Although E. corylata is still very widespread and common throughout much of Britain and Ireland, there has been a significant decline in both its abundance and distribution since 1970 (Randle et al., 2019).Its global distribution extends across Europe and Asia to Japan (GBIF Secretariat, 2023).
Here we present a chromosomally complete genome sequence for E. corylata based on one male specimen from Wytham Woods, Oxfordshire, UK.The genome of E. corylata 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.A genome sequence for E. corylata will contribute to a growing data set of resources for understanding lepidopteran biology.

Genome sequence report
The genome was sequenced from one male Electrophaes corylata (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 70-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 3 missing joins or mis-joins and removed 3 haplotypic duplications, reducing the scaffold number by 7.89%. The final assembly has a total length of 347.5 Mb in 34 sequence scaffolds with a scaffold N50 of 12.7 Mb (Table 1).Most (99.97%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/934936.

Sample acquisition and nucleic acid extraction
The specimen used for genome assembly was a male Electrophaes corylata (specimen IDO x001879, individual ilEleCory1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.32) on 2021-05-28 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
The sample was prepared for DNA extraction at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEleCory1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.

Sequencing
Pacific Biosciences HiFi circular consensus and DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from head and   thorax tissue of ilEleCory1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Electrophaes corylata assembly (GCA_947095575.1) in Ensembl Rapid Release.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome    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 The genome sequence is released openly for reuse.The Electrophaes corylata 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.

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Insect genome I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
Reviewer Report 11 September 2023 https://doi.org/10.21956/wellcomeopenres.21743.r65866 The assembly was produced using world leading approaches: PacBio Hi-Fi reads and scaffolding with Hi-C.The resulting assembly is of excellent quality by all metrics.An annotation was performed based on homology alone (RNA-seq data was no used), but it appears to have very high accuracy.
I have no concerns about the manuscript or the resource described.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Evolutionary genomics, population genomics I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Electrophaes corylata, ilEleCory1.1: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 347,554,160 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 (17,402,341 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (12,663,981 and 8,126,972 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/Electrophaescorylata/ dataset/CAMUPP01/snail.

Figure 3 .
Figure 3. Genome assembly of Electrophaes corylata, ilEleCory1.1: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/Electrophaescorylata/dataset/CAMUPP01/blob.
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.

Figure 4 .
Figure 4. Genome assembly of Electrophaes corylata, ilEleCory1.1: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/Electrophaescorylata/dataset/ CAMUPP01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Electrophaes corylata, ilEleCory1.1:Hi-C contact map of the ilEleCory1.1 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=SgopR3ypQ8mwld1Kv6Uerg.