The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794)

We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 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 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.


Background
A common micro-moth of the family Tortricidae, the Pandemis corylana is noted for its net-like pattern or reticulation to the yellow and reddish-brown and dark cross banding of the forewing.Found in most of England and Wales and local in Scotland and Ireland, the single-brooded, Pandemis corylana is on the wing from July to September, occasionally to October.Its larvae feed on trees and shrubs from May to July in deciduous woodland, scrub, hedgerows and gardens and may be found in spun or folded leaves of hazel, ash, oak, bramble and honeysuckle (Sterling et al., 2012).
There are five similar Pandemis species in the UK, with identification assisted by raising of larvae, and dissection of adults (British Lepidoptera, 2023;Kimber, 2023).Worldwide there are multiple species of Pandemis, including some important pests on apple.Dombroskie and Sperling (2012) highlighted the importance of a combined approach, using DNA, morphological and geographic evidence to successfully separate similar species where no single source was sufficient.This is an example of areas of work where the completed genome sequence will provide additional evidence.
We present a chromosomally complete genome sequence for Pandemis corylana based on one male specimen from Wytham Woods, Oxfordshire, UK, as part of the Darwin Tree of Life Project.This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Genome sequence report
The genome was sequenced from one male Pandemis corylana (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 47-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 32 missing joins or mis-joins and removed 10 haplotypic duplications, reducing the scaffold number by 2.44%. The final assembly has a total length of 441.6 Mb in 39 sequence scaffolds with a scaffold N50 of 15.7 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 (99.93%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome.Chromosome Z was assigned by synteny to Pandemis cinnamomeana (GCA_932294345.1)(Boyes et al., 2023).Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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.

Sample acquisition and nucleic acid extraction
A male Pandemis corylana (specimen ID Ox000682, ToLID ilPanCory1) was collected from Wytham Woods, Oxfordshire (biological vice-country Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-20 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.The specimen used for Hi-C sequencing (specimen ID NHMUK013805966, ToLID ilPanCory2) was collected from Hartslock Nature Reserve, England, UK (latitude 51.51, longitude -1.11) on 2021-07-29 using a light trap.The specimen was collected by Ian Sims and identified by Ian Sims and David Lees (Natural History Museum) and preserved on dry ice.et al., 2023).The sample was homogenised using a Nippi Powermasher fitted with a BioMasher pestle (Denton et al., 2023a).HMW DNA was extracted using the Automated MagAttract v1 protocol (Sheerin et al., 2023).HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30 (Todorovic et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation (Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.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.

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 head and thorax tissue of ilPanCory2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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 Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Pandemis corylana assembly (GCA_949127965.1) 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

Tyler Scott Alioto
Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain This genome note reports the specimen collection, sequencing, genome assembly and annotation of the chequered fruit-tree tortrix, Pandemis corylana.The genome note is complete, wellorganized and well-written.Standard state-of-the-art methods were used to achieve a high-quality chromosome-level primary assembly (as well as the mitogenome, alternate haplotypes and a Wolbachia symbiont) that meet the minimum EBP reference genome standards.All data has been deposited in the INSDC and protocols, quality control info (tolqc), and analyses have been made public.
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: Genome assembly, genome annotation, gene prediction 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 Pandemis corylana, ilPanCory1.1: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 441,605,538 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 (37,479,866 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (15,684,937 and 10,157,545 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/Pandemis%20corylana/dataset/ilPanCory1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Pandemis corylana, ilPanCory1.1:Hi-C contact map of the ilPanCory1.1 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=ZXEiFv_ASrm4DroJa5smuw.

Table 2 . Chromosomal pseudomolecules in the genome assembly of Pandemis corylana, ilPanCory1. INSDC accession Chromosome Length (Mb) GC%
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