The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795)

We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 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 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.


Background
The Small Emerald (Hemistola chrysoprasaria) is a geometrid moth with rounded wings (17-20mm forewing length) and white cross-lines on an overall blue-green background.The background colour is bright when newly emerged, but fades to almost white over time.H. chrysoprasaria has a Palaearctic distribution, and is widely distributed in the south of England and Wales.There is one generation per year, with a peak flight time of June to August in the UK, and overwintering occurs at the larval stage.Larvae feed primarily on Traveller's joy (Clematis vitalba), although they may also feed on other species of Clematis (Waring et al., 2017).Transport on cultivated plants may explain sporadic reports of small emeralds outside of the "normal" range (for example, Scotland (NBN Atlas Partnership, 2023).The conservation status of H. chrysoprasaria in Great Britain was assessed as "least concern" in 2019 (Fox et al., 2019), a potentially encouraging change from "vulnerable" in 2006"vulnerable" in (Conrad et al., 2006;;Fox et al., 2006), and "declining" in 2013(Fox, 2013).
H. chrysoprasaria larvae show an interesting colour change phenomenon, changing from brown during late summer to green in spring, following a period of winter diapause.Such background-matching larval colour change behaviour is known from other species of Lepidoptera, such as the Peppered Moth (Biston betularia), where extraocular photoreception is used to determine background colouration (Eacock et al., 2017;Eacock et al., 2019).However, the Peppered Moth example seems to be an adaptation to larval dispersal via wind and polyphagy, where larvae can settle on a diverse range of host plants, rather than a temporal change on a single host plant as is the case for H. chrysoprasaria.This Small Emerald genome sequence assembly will provide a useful resource for the identification of the molecular basis of this colour change behaviour.

Genome sequence report
The genome was sequenced from one male Hemistola chrysoprasaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 49-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 17 missing joins or misjoins and removed 3 haplotypic duplications, reducing the scaffold number by 8.57%. The final assembly has a total length of 438.2 Mb in 31 sequence scaffolds with a scaffold N50 of 16.1 Mb (Table 1).Most (99.98%) 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-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.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/934942.

Sample acquisition and nucleic acid extraction
A male Hemistola chrysoprasaria (specimen ID Ox001665, ToLID ilHemChry1) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.31) on 2021-07-17, using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilHemChry1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Abdomen tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW)   ( Bernt et al., 2013) 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 (Rhie et al., 2020).This work was

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Hemistola chrysoprasaria assembly (GCA_947063395.1) 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

Fathiya Khamis
International Centre of Insect Physiology and Ecology Nairobi, Nairobi, Kenya

Inusa Ajene
International Centre of Insect Physiology and Ecology, Nairobi, Kenya The data note titled "The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795)" presents the genome assembly of the Small Emerald (Hemistola chrysoprasaria) moth.The paper is thorough, describing the background of the insect, the genome assembly and annotation.The methods are clearly described, and the protocols used are current and technically sound with publicly available references to databases and software.This is a good paper with impact as a potential resource for future genomic studies on the biology of the moth and the molecular basis of the colour change behaviour in the larvae.

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: Molecular Biologist
We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Chuanlin Yin
China Jiliang University, Hangzhou, China The authors conducted a thorough genome sequencing of the small emerald, Hemistola chrysoprasaria.The results are promising, and the methods are clearly outlined.This paper has reached a publishable level, but there are a few minor issues that should be addressed to further improve it.

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Genome annotation: the BRAKER2 pipeline was used in default protein mode to generate annotation, what the homology protein sets did the authors used, need to specify.

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Table 3: the braker software is missing.

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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: Insectomics and 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.

Figure 2 .Figure 3 .
Figure 2. Genome assembly of Hemistola chrysoprasaria, ilHemChry1.1: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 438,253,172 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 (30,684,051 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (16,143,413 and 10,750,662 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/ilHemChry1.1/dataset/CAMSTX01/snail.

Figure 5 .
Figure 5. Genome assembly of Hemistola chrysoprasaria, ilHemChry1.1:Hi-C contact map of the ilHemChry1.1 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=b59mEK0zS3C-ucZrQBgUWg.

Reviewer Report 06
August 2024 https://doi.org/10.21956/wellcomeopenres.22145.r89120© 2024 Yin C.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Table 1 . Genome data for Hemistola chrysoprasaria, ilHemChry1.1. Project accession data
C:98.2%[S:97.8%,D:0.4%],F:0.4%,M:1.3%,n:5,286C≥95%DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.SequencingPacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific

Table 3
contains a list of relevant software tool versions and sources.