The genome sequence of the Winter Shade, Tortricodes alternella [Denis & Schiffermüller], 1775

We present a genome assembly from an individual male Tortricodes alternella (the Winter Shade; Arthropoda; None; Lepidoptera; Tortricidae). The genome sequence is 441.2 megabases in span. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,280 protein coding genes.


Background
Tortricodes alternella, the Winter Shade or Spring Harbinger, is a moth of the Tortricidae family (Sterling et al., 2023).It has a wingspan of 19-23mm and narrow forewings for a tortrix which are a variably marked in shades of grey/yellow brown with a darker cross-band, whilst the hindwings are pale brown with darker veins.Females are darker with less distinct markings (Sterling et al., 2023).It is one of the earliest tortricids on the wing, between late January and April, and will come to light (Sterling et al., 2023).Larvae of T. alternella are up to 15mm long, with a brown head and reddish-brown dorsal surface of the abdomen with white pinacula and dorsal and subdorsal lines, whilst the ventral surface is pale yellow.They feed on various deciduous trees in May and June but predominantly on oaks (Quercus spp.) and hornbeams (Carpinus spp.), where they feed within leaves they have spun together (Kimber, 2024).
T. alternella is classified as common in Britain (Davis, 2012).It is found in woodland habitats, and sometimes scrub or gardens, throughout England and Wales but is considered local in Scotland and Ireland (Sterling et al., 2023).Globally, the species is distributed across Europe, between southern Scandinavia and the Mediterranean over to the Balkan Peninsula, with scattered records into western Asia (GBIF Secretariat, 2024).
The genome of the winter shade, Tortricodes alternella, was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomal-level genome sequence for Tortricodes alternella, based on a male specimen from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from a male Tortricodes alternella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 58-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 8 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the scaffold number by 3.70%. The final assembly has a total length of 441.2 Mb in 25 sequence scaffolds with a scaffold N50 of 18.8 Mb (Table 1).The snail plot 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 (99.98%) of the assembly sequence was assigned to 22 chromosomal-level scaffolds, representing 21 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 Eudemis profundana (GCA_947034925.1)(Boyes et al., 2023).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
Specimens of Tortricodes alternella were collected from Wytham Woods, Oxfordshire (biological vice-country Berkshire), UK (latitude 51.77, longitude -1.34) on 2022-03-07 using a   RNA was extracted from ilTorAlte2 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers'     et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Table 3. Software tools: versions and sources.

Software tool
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 Tortricodes alternella assembly (GCA_947859335.1) in Ensembl Rapid Release at the EBI.

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 I reviewed the manuscript "The genome sequence of the Winter Shade, Tortricodes alternella" .
Authors explain methods well and also provide information to find full protocols, which allow replication of the study.This is the first contribution of a complete genome for the genus Tortricodes.
Authors mentioned that the mitogenome assembly is within the multifasta file of the genome submission; however, i recommend to upload it separately with annotation so it can be retrieved in NCBI when blasting.Also, if possible, I recommend providing better-quality imaging of specimens used in the study.

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: entomolgy, genomics, phylogenomics, systematics 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.

Rudolf Meier
Humboldt University, Berlin, Germany The manuscript describes the draft genome sequence of Tortricodes alternella.I have few suggestions for improvement: (1) The Abstract includes "(the Winter Shade; Arthropoda; None; Lepidoptera; Tortricidae)."Presumably, there is something wrong with the "None" part.
(2) The following sentence under Background should be split: "It has a wingspan of 19-23 mm and narrow fore wings for a tortrix which are a variably marked in shades of grey/yellow brown with a darker cross-band, whilst the hind wings are pale brown with darker veins." (3) Rephrase: "It is one of the earliest tortricids on the wing, between late January and April, and will come to light" given that the report is also for genome biologists.
(4) You reference the "GBIF Secretariat, 2024" instead of providing the species link in GBIF.
(5) The species have several DNA barcodes in NCBI.I would recommend that the statement about species identification by Liam Crowley is complemented with a statement that the COI sequences also match the DNA barcodes for the species followed by the relevant access numbers.

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: entomology, species discovery

Figure 2 .
Figure 2. Genome assembly of Tortricodes alternella, ilTorAlte1.1:metrics.The BlobToolKit snail plot 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 441,253,704 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 (39,282,859 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,827,800 and 13,942,425 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/CANUEM01/dataset/CANUEM01/snail.

Figure 3 .
Figure 3. Genome assembly of Tortricodes alternella, ilTorAlte1.1: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/CANUEM01/dataset/CANUEM01/blob.

Figure 4 .
Figure 4. Genome assembly of Tortricodes alternella, ilTorAlte1.1: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/CANUEM01/dataset/CANUEM01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Tortricodes alternella, ilTorAlte1.1:Hi-C contact map of the ilTorAlte1.1 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=O018ksByT3uuMeswRXz6jQ.

Table 2 . Chromosomal pseudomolecules in the genome assembly of Tortricodes alternella, ilTorAlte1. INSDC accession Chromosome Length (Mb) GC%
(Allio et al., 2020)he 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)andPretextView (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi(Uliano-Silva et al., 2023), which runs MitoFinder(Allio et al., 2020)or MITOS (Bernt 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.
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.