The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796)

We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.


Background
The Brown Oak Tortrix, Archips crataeganus (Hübner, 1796), from the family Tortricidae is found in Europe, Asia Minor and north-western Africa.The East Asian (South Korea, Japan, China: Heilongjiang, Jilin, Shaanxi, Sichuan) subspecies, A. crataegana endoi, was described by Yasuda (1975).In the UK, A. crataegana is classified as 'local'; uncommon but with a wide distribution over much of the British Isles (Davis, 2012).In the UK, Archips crataegana is mainly found in wooded habitats and has one generation per year.Adults fly between June and August.This species is sexually dimorphic (Szabóky & Csóka, 2010); females are larger than males.Males have light brown forewings with dark brown markings, females tend to have darker forewings with obscured markings (Bradley et al., 1973).Females deposit egg masses on the bark of a variety of deciduous trees, including Quercus, Betula, Fraxinus and Salix species (Szabóky & Csóka, 2010).The egg masses resemble bird droppings, and the eggs overwinter (Szabóky & Csóka, 2010).The larvae (particularly the later instars) feed inside tightly rolled leaves (Szabóky & Csóka, 2010).Pupation occurs at the final larval feeding site.Like other members of the genus Archips, the larvae of this species are polyphagous pests of fruit and forest trees, causing damage to leaves, blossoming buds, flowering buds and flowers (Meijerman & Ulenberg, 2000).
The genome of the Brown Oak Tortrix, Archips crataeganus, 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 chromosomally complete genome sequence for Archips crataeganus, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Archips crataeganus (Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (51.77,.A total of 36-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 38 missing joins or mis-joins and removed 7 haplotypic duplications, reducing the scaffold number by 50%, and increasing the scaffold N50 by 3.1%. The final assembly has a total length of 626.9 Mb in 31 sequence scaffolds with a scaffold N50 of 21.6 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 (99.99%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 29 autosomes and the W and Z sex chromosomes.There is some uncertainty to the order and orientation of W chromosome contigs.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 female Archips crataeganus (specimen ID Ox001685, ToLID ilArcCraa1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2021-07-17 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation; DNA extraction; HMW DNA fragmentation; and

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 and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
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 calculated in Merqury (Rhie et al., 2020).This work was done using Nextflow (Di Tommaso et al., 2017)  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 Archips crataeganus assembly (GCA_947859365.1) in Ensembl Rapid Release.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 • Legality of collection, transfer and use (national and international) 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.

Andrew Mongue
University of Florida, Gainesville, Florida, USA Once again, another well assembled lepidopteran genome.I am very excited about the increasing number of W chromosomes captured by the DTOL project and commend the authors for their work assembling such messy chromosomes.
I am somewhat confused about the gene annotation side of this project however.The manuscript mentions a BRAKER2 annotation, but provides very little detail on how this was approached (e.g. was the assembly repeatmasked first?).Moreover, when checking the available data, it looks like RNA sequencing was generated (see: https://tolqc.cog.sanger.ac.uk/darwin/insects/Archips_crataeganus/) but it's unclear to me whether or not these RNA data were used in the annotation.
I recently reviewed another genome note with essentially the same lack of clarity around the annotation, so I hope this and future genome notes provide more detail on this front to make the most of the resources generated.
Is the rationale for creating the dataset(s) clearly described?

Sean T S Law
The Chinese University of Hong Kong, Hong Kong, Hong Kong This article presents the genome of a female Brown Oak Tortrix, Archips crataeganus.The genome is ~627 Mb in size with scaffolds anchored into 31 pseudomolecules, including the Z and W sex chromosomes as the first two largest chromosomes.The high completeness and continuity of the genome assembly were supported by BUSCO score of 98.2% and N50 statistics.In summary, the genome assembly of A. crataeganus is of high-quality.

Annabel Whibley
1 The University of Auckland, Auckland, Auckland, New Zealand 2 Bragato Research Institute, Blenheim, New Zealand The authors report a chromosomally-complete assembly of the Brown Oak Tortrix moth using PacBio HiFi reads (run on the Sequel II platform) and an Illumina Hi-C dataset.The resulting assembly and methods are clearly presented, using DToL protocols and pipelines.The assembly statistics are impressive and include 100% k-mer completeness.The HiC map looks phenomenal and the quality of this assembly will make it a wonderful resource for the community.
I have just very minor comments: Archips could be abbreviated throughout the manuscript after its first introduction.And while the protocols and reporting in these assembly notes are very succinctly and tightly composed, at times they are perhaps too sparse.For example, I would like to see the kmer size used in Merqury noted (the default in FastK upstream of the MerquryFK is 40, whereas the original Merqury Meryl implementation is typically used with 19/21-mers when assessing the accessory script is provided; k-mer choice has an impact on the reported completeness).
In previous reports I have noted that the HiC reporting states that YAHS is used to scaffold without describing the alignment and processing steps prior to invoking YAHS, when the YAHS Github documentation notes that there are multiple routes to generating the inputs.
Is the rationale for creating the dataset(s) clearly described?

Figure 2 .Figure 3 .
Figure 2. Genome assembly of Archips crataeganus, ilArcCraa1.1: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 626,923,680 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 (51,685,801 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (21,612,927 and 13,401,462 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/Archips%20crataeganus/dataset/ilArcCraa1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Archips crataeganus, ilArcCraa1.1:Hi-C contact map of the ilArcCraa1.1 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=E3hPUivPSOK66eemQfiTVA.

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? Partly Are the datasets clearly presented in a useable and accessible format? Partly 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, however I have significant reservations, as outlined above.
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.

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.
https://doi.org/10.21956/wellcomeopenres.22601.r72743