The genome sequence of the Feathered Ranunculus, Polymixis lichenea (Hübner, 1813)

We present a genome assembly from an individual male Polymixis lichenea (the Feathered Ranunculus; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 716.7 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 15.48 kilobases in length.


Background
The Feathered Ranunculus, Polymixis lichenea (Hubner, 1813) is a moderate sized noctuid moth with a wingspan of about 35-40 mm.Its forewings have a greenish tint, finely dotted with grey.The orbicular and reniform markings sometimes stand out with whitish margins or centres, as does occasionally a darker median fascia enveloping them; subterminal markings also include darker marks and other cross lines intermingle lighter and darker highlights.Local forms may be paler, darker, yellower or greener, apparently varying with substrate.Hindwings are dorsally darker in the female.The adult male, which tends to fly after midnight (Skinner & Wilson, 2009), has pectinate antennae, as suggested by the vernacular name.The moth's flight period is in the Palaearctic Autumn, in the UK from August to October (Randle et al., 2019), and it overwinters as a small larva (Waring et al., 2017).
P. lichenea exhibits a single mitochondrial cluster on BOLD, BOLD:AAH7735 (24/08/2023) with UK populations closer to those of Norway than the Mediterranean ones which are up to 1.38% divergent from them (maximum intraspecific divergence 1.77%).Several near neighbours of P. lichenea on BOLD belonging to different genera include species of Mniotype Franclemont, 1941, Fishia Grote, 1877and Dryotype Hampson, 1906, whilst Polymixis polymita (Linnaeus, 1761) (the type species of Polymixis Hübner, [1820]) is at least 6.27% pairwise divergent to it in COI-5P (24/08/2023).Polymixis is a member of the noctuine tribe Xylenini, and (Fibiger et al., 2001) place P. lichenea in the subgenus Eumichtis Hübner, 1821.Resolving the phylogenetic relationships of Polymixis will require multiple loci, which the genome sequence presented here will help to provide.

Genome sequence report
The genome was sequenced from one male Polymixis lichenea (Figure 1) collected from Restharrow Dunes National Nature Reserve, England, UK (51.27,1.38).A total of 40-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 nine missing joins or mis-joins and removed two haplotypic duplications, reducing the scaffold number by 4.65%.
The final assembly has a total length of 716.7 Mb in 40 sequence scaffolds with a scaffold N50 of 24.4 Mb (Table 1).Most (99.94%) 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).Z chromosome identified based on synteny with Fissipunctia ypsillon (GCA_947568875.1)and Dryobota labecula (GCA_947523025.1).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.
The estimated Quality Value (QV) of the final assembly is 67.1 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 99.1% (single = 98.6%, duplicated = 0.5%), using the lepidoptera_odb10 reference set (n = 5,286).The sample weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Head and thorax tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.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 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    et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Software tool Version
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

Tianzhu Xiong
Cornell University, Ithaca, USA The article presents a chromosome-level genome assembly of the Noctuid moth Polymixis lichenea.Methods based on PacBio and Hi-C are well described.I manually checked their Hi-C map and could not find obvious assembly errors.Based on other data presented here such as BUSCO, this is a high-quality reference genome.
Is the rationale for creating the dataset(s) clearly described?

Kuppusamy Sivasankaran
Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India I appreciate the authors for assembling the Polymixis lichenea whole genome sequence.The authors have used the proper software for assembly and annotation of the genome.
Comments: Page no. 3 -In the second paragraph, the second line "is a moderately sized noctuid" can be changed to "is a moderately sized Noctuid" 1.
Page no. 3 -The second paragraph's third line can be changed to "Forewing greenish tint, finely dotted with grey". 2.
Page no. 3 -sixth paragraph second column 4 th line there is a typo error.place P. lichenea in the….alphabet'i' is in italics.It can be changed to a normal letter.

Question:
Why do authors not annotate the genome of P. lichenea?In the genome annotation authors could get the number of coding genes, non-coding genes, and transcript genes.
○ Overall, the manuscript can be accepted for indexing.

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: Mitochondrial genome sequencing for phylogenetic study 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.
P. lichenea is distributed towards coasts locally in the Western Palaearctic only, but absent in western Ireland and most of northern Britain (Randle et al., 2019), and ranges from north-east Ireland to the northern Baltic, Spain and Southern France but missing in central Europe and Scandinavia, with records in the Canaries and north-west Africa: Morocco (GBIF Secretariat, 2022).Populations in the UK have declined by 39% in abundance between 1970 and 2016 and by 21% in distribution (Randle et al., 2019).Between 1968 and 2006 Rothamsted trap numbers declined annually by an average of about 0.7% (Conrad

Figure 2 .
Figure 2. Genome assembly of Polymixis lichenea, ilPolLich1.1: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 716,694,765 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 (59,173,276 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (24,363,533 and 17,269,570 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/ilPolLich1.1/dataset/CARWXJ01/snail.

Figure 5 .
Figure 5. Genome assembly of Polymixis lichenea, ilPolLich1.1:Hi-C contact map of the ilPolLich1.1 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=W7Awu15tSs2lO-z-wTKsJA.

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

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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
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.