The genome sequence of the Blood-vein moth, Timandra comae Schmidt, 1931

We present a genome assembly from an individual male Timandra comae (the Blood-vein; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 334.4 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 15.91 kilobases in length.


Background
The Blood-vein Timandra comae is a moth in the family Geometridae and, as such, has a thin body and wide triangular wings.It is distinguished from other moths in the United Kingdom by the pale creamy-buff wings with a straight pink or brownishred line which runs from the tip of the forewing to its trailing edge and across the hindwing.The trailing edge of both wings is pinkish-red and there are varying amounts of fine dark speckling across both wings (Waring et al., 2017).However, there is a very similar species Timandra griselata, found in Scandinavia, that has greyish speckling on a whitish forewing background, rather than the more yellowish colour seen in T. comae: there are slight differences in the female genitalia, but no differences between those of the males, and the two species are separable by DNA sequencing of the mitochondrial COI locus (Õunap et al., 2005).
In the United Kingdom T. comae's range is mainly restricted to the south of the country, as far north as the Scottish Borders, its having recently reached Cumberland and Northumbria: although there are records from Scotland these moths are considered immigrants, with those found in Orkney and Shetland thought to be Scandinavian in origin (Waring et al., 2017).
Timandra comae has two generations a year, although it may have three in the south, where these generations may overlap, and overwinters as a larva (Waring et al., 2017).The larvae feed on Docks Rumex spp., Oraches Atriplex spp., Common Sorrel Rumex acetosa, Sheep's Sorrel Rumex acetosella, and Knotgrass Polygonum aviculare (Kurze et al., 2018;Skinner & Wilson, 2009;Waring et al., 2017).The application of nitrogen fertiliser, increasing the nitrogen levels in Sheep's Sorrel, has been shown to decrease the survival rate of the larvae of T. comae by more than two-thirds, compared to the control group, and was thought to be a possible mechanism leading to the decline of some species (Kurze et al., 2018).
We present a chromosomally complete genome sequence for Timandra comae, based on one specimen collected using a mercury vapour light trap in a rural garden in the hamlet of Bratton, near Minehead, in Somerset, as part of the Darwin Tree of Life Project.

Genome sequence report
The genome was sequenced from one male Timandra comae (Figure 1) collected from Bratton, Somerset, UK (51.20,.A total of 84-fold coverage in Pacific Biosciences singlemolecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 19 missing joins or mis-joins and removed 5 haplotypic duplications, reducing the assembly length by 0.45% and the scaffold number by 11.11%. The final assembly has a total length of 334.4 Mb in 39 sequence scaffolds with a scaffold N50 of 11.5 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.92%) 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 5; Table 2).The Z chromosome was identified based on synteny with Cyclophora punctaria (GCA_951394245.1).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.

Sample acquisition and nucleic acid extraction
A male Timandra comae (specimen ID Ox002231, ToLID ilTimComa1) was collected from Bratton, Somerset, UK (latitude 51.20, longitude -3.51) on 2022-06-20 using a light trap.The specimen was collected and identified by Denise Wawman (University of Oxford), and then preserved on dry ice.

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 a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from remaining head and thorax tissue of ilTimComa1 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., 2023), which runs MitoFinder (Allio 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.
Table 3 contains a list of relevant software tool versions and sources.

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 The analyzed specimen is a male.
The article make statements of 1) the two above-mentioned species being separable in their DNA barcodes and 2) that T. griseata is Scandinavian.Both cannot be true, because the cluster of griseata is found in UK by many specimens in BOLD.
The article undoubtedly lists reported food plants of T. comae as mentioned in literature, but there tend to be lots of errors, and in this case I would strongly question Atriplex spp.being among the food plants.
As shown in the snailplot graph of Figure 2

Kay Lucek
University of Neuchâtel, Neuchâtel, Switzerland The authors present the chromosome level genome assembly of a male specimen of the blood vein moth Timandra comae.The assembly consists of 31 chromosomes including the Z chromosome.The assembly is highly complete as revealed by the high BUSCO score but not fully phased.Sequencing and genome assembly follow the current state of the art and use established methods.
Overall, the presented assembly will be of great value to study genome architecture as well as genome size evolution in Lepidoptera.I particularly appreciate the biological background given for this species, where the reference genome provides the opportunity to study the range expansion of this species in the UK and elsewhere.
Is the rationale for creating the dataset(s) clearly described?Yes GSReport, 2nd paragraph.Here it is stated that the assembly contains 39 scaffolds.The number is the same as in table 1, but in Figure 2, 3 and 4 it is stated that the assembly consists of 40 scaffolds.Maybe I misunderstood something, but check if it is correct.

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 I confirm that I have read this submission and believe that I have an appropriate level of

Figure 2 .
Figure 2. Genome assembly of Timandra comae, ilTimComa1.1: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 334,373,444 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 (19,455,470 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (11,490,666 and 8,097,011 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/ilTimComa1_1/dataset/ilTimComa1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Timandra comae, ilTimComa1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilTimComa1_1/dataset/ilTimComa1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Timandra comae, ilTimComa1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilTimComa1_1/dataset/ilTimComa1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Timandra comae, ilTimComa1.1:Hi-C contact map of the ilTimComa1.1 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=M7k_mdjfQq-QeuG4VyopUg.
Are the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesNiclas BackströmUppsala University, Uppsala, Sweden Minor comments: Background, 2nd paragraph."its having" sounds a bit odd -consider editing Background, 4th paragraph.Unclear what "chromosomally complete" really means.Consider editing.
(Bates et al., 2023)) molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the ilTimComa1 sample was weighed and dissected on dry ice(Jay et al., 2023).Tissue from the head and thorax was homogenised using a PowerMasher II tissue disruptor(Denton et al., 2023a).HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol(Oatley et al., 2023).The DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31(Bates et al., 2023).Sheared

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:
and other graphs, the published genome is clearly of high standard.This is indicated e.g. by high BUSCO coverage (only 1.2% missing) and scaffold statistics that indicate high quality.No competing interests were disclosed.

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 2024 https://doi.org/10.21956/wellcomeopenres.23328.r98735© 2024 Lucek K.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.