The genome sequence of the silver Y moth, Autographa gamma (Linnaeus, 1758)

We present a genome assembly from an individual female Autographa gamma (the silver Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 373 megabases in span. The majority of the assembly (99.65%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled and is 15.2 kilobases in length.


Background
Autographa gamma (silver Y) is a widespread and common noctuid moth found across the Palaearctic from Europe to Japan, and also in North Africa.The adult moth is commonly seen visiting nectar-rich flowers at dusk or in the daytime in late summer; the species also flies at night and is attracted to light. A. gamma is resident through winter only in the southern part of its range, but is highly migratory with large numbers of individuals moving north across Europe during spring and summer.
The impressive long distance migration is achieved through moths selecting fast-moving airstreams 200-1000 metres above ground, coupled with an internal compass sense so that flight is restricted to nights with favourable winds (Chapman et al., 2008;Chapman et al., 2010).The migrating adults breed in high-latitude areas such as the UK to boost numbers further.Adults fly south in autumn to overwinter in southern Europe.Use of vertical-facing entomological radar coupled with insect trapping has revealed that the number of A. gamma adults reaching the UK varies from 10 million to over 200 million adult moths each year (Chapman et al., 2008).The sporadic occurrence of huge numbers often brings A. gamma to wider attention.For example, during the Euro 2016 football final in Paris, prolonged use of floodlights attracted clouds of A. gamma, with moths settling on Cristiano Ronaldo and other players while watched by a television audience of over 280 million.
The larvae of A. gamma feed a wide range of herbaceous plants including clover and nettle; the larvae can also cause damage to cultivated crops notably lettuce, sugar beet, tomatoes, peas and cabbage (Carter, 1984;Golikhajeh et al., 2016).Two female sex pheromone components have been identified (Dunkelblum & Gothilf, 1983) with similarity to the pheromone blends of closely related noctuid moths (Becher & Revadi, 2020).The availability of a genome sequence will aid future research into migratory behaviour, pheromone production and chemoreception.
The genome of A. gamma was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all of the named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for A. gamma, based on one specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a single female A. gamma (ilAutGamm1; Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-country: Berkshire), UK (latitude 51.775, longitude -1.332).A total of 36-fold coverage in Pacific Biosciences single-molecule long reads and 119-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 20 missing/misjoins and removed 2 haplotypic duplications, reducing the assembly size by 0.06% and the scaffold number by 16.39%, and increasing the scaffold N50 by 6.60%.
The final assembly has a total length of 373 Mb in 102 sequence scaffolds with a scaffold N50 of 12.2 Mb (Table 1).Of the assembly sequence, 99.65% was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the W and Z sex chromosomes (Figure 2-Figure 4; Table 2).The W chromosome is highly fragmented.The assembly has a BUSCO (Manni et al., 2021) completeness of 98.8% (single 98.6%, duplicated 0.3%) using the lepidoptera_odb10 reference set (n=5286).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
One female A. gamma (ilAutGamm1) and one A. gamma of unknown sex (ilAutGamm2) were collected from Wytham Woods, Oxfordshire, UK (latitude 51.772, longitude -1.338) by Douglas Boyes, UKCEH, from woodland using a light trap.The specimen was identified by the same individual and preserved on dry ice.
DNA was extracted from head/thorax tissue at the Wellcome Sanger Institute (WSI) Scientific Operations core from the whole organism using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.RNA was extracted from abdomen tissue of ilAutGamm1 and ilAutGamm2 in the Tree of Life Laboratory at the WSI using TRIzol (Invitrogen), according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration RNA assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II (HiFi), Illumina HiSeq X (10X) and Illumina HiSeq 4000 (RNA-Seq) instruments.Hi-C data were generated from abdomen tissue of ilAutGamm1 using the Qiagen EpiTect Hi-C kit and sequenced on HiSeq X.

Genome assembly
Assembly was carried out with HiCanu (Nurk et al., 2020); haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).One round of polishing was

Muzafar Riyaz
Xavier Research Foundation, St Xavier's College, Palayamkottai, Tamilnadu, India The article titled "The Genome Sequence of the Silver Y Moth, Autographa gamma (Linnaeus, 1758)" provides a comprehensive overview of the genome assembly of Autographa gamma, a widespread and common noctuid moth.The detailed assembly, sequencing methodology, and insights into the species' behavior contribute to both scientific knowledge and potential applications in agriculture and pest management.

Yan-Qun Liu
Shenyang Agricultural University, Shenyang, Liaoning, China This paper reported a chromosomal-level genome assembly from Autographa gamma, a widespread and common Noctuidae moth, that is helpful for understanding the genetic information of this species.Two minor revisions should be addressed.1.It is better to add the information of scaffold numbers for each pseudomolecule. .2. Species in Table 1.Phlogophora meticulosa = Autographa gamma.
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: Insect Genetics and 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.
benefit future studies of the silver Y moth.W chromosome is rarely assembled in other Lepidoptera genomes.However, methods for identifying sex chromosomes have not been 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: Molecular ecology, population genetics, 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 1 .
Figure 1.Image of the ilAutGamm1 specimen taken prior to preservation and processing.

Figure 2 .
Figure 2. Genome assembly of Autographa gamma, ilAutGamm1.1: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 373,067,087 bp assembly.The distribution of chromosome lengths is shown in dark grey with the plot radius scaled to the longest chromosome present in the assembly (19,124,284 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 chromosome lengths (12,167,202 and 6,891,251 bp), respectively.The pale grey spiral shows the cumulative chromosome 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/ilAutGamm1.1/dataset/CAJHUD01/snail.

Figure 3 .
Figure 3. Genome assembly of Autographa gamma, ilAutGamm1.1:cumulative sequence.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/ilAutGamm1.1/dataset/ CAJHUD01/cumulative.
Table 3 contains a list of all software tool versions used, where appropriate.
(Allio et al., 2020)L, HiGlass(Kerpedjiev et al., 2018)and Pretext.The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2021), which performed annotation using MitoFinder(Allio et al., 2020).The genome was analysed and BUSCO scores generated within the BlobToolKit environment(Challis et al., 2020).Darwin Tree of Life Project Sampling Code of Practice.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

Table 3 . Software tools used.
to, the Darwin Tree of Life Project.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 genome sequence is released openly for reuse.The A. gamma 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.The genome will be annotated using the RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute.Raw data and assembly accession identifiers are reported in supplied

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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.

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.

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.