The genome sequence of the Heath Knot-horn, Apomyelois bistriatella (Hulst, 1887)

We present a genome assembly from an individual female Apomyelois bistriatella (the Heath Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 389.6 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.2 kilobases in length.


Background
Apomyelois bistriatella (Hulst, 1887) is a moth of the Pyralidae family.It has a circumpolar distribution, being found across North America and northern Eurasia, ranging from the British Isles in the west to Hokkaido in the east (GBIF Secretariat, 2022;Neunzig, 1990).In Europe it is represented by the subspecies neophanes (Goater et al., 1986;Neunzig, 1990).The species has a scattered distribution in the British Isles, favouring heathy locations (Goater et al., 1986;Parsons & Davis, 2018).
Within the British Isles, larvae have been recorded feeding within the fungus Daldinia concentrica, growing on burnt Gorse (Ulex europeaus) or young birches (Betula) (Goater et al., 1986), however in North America the species is also known to feed within Hypoxylon fungi, growing on recently killed oak (Quercus) or poplar (Populus) (Neunzig, 1990).Larvae feed between August and October, after which the larva burrows into dead wood or fungus and overwinters (Goater et al., 1986;Parsons & Davis, 2018).Pupation occurs during May (Parsons & Davis, 2018).Adults fly at night between May and September, resting by day on tree trunks with the head raised away from the body and the tips of the forewings pressed against the trunk (Goater et al., 1986;Parsons & Davis, 2018).Colonies of this species are ephemeral, and can move around according to the availability of young birch and burnt gorse (Goater et al., 1986).
The genome of Apomyelois bistriatella 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 Apomyelois bistriatella, based on one female specimen of the subspecies neophanes from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Apomyelois bistriatella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34).A total of 70-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 or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 13.16%.
The final assembly has a total length of 389.61 Mb in 33 sequence scaffolds with a scaffold N50 of 13.7 Mb (Table 1).Most (99.99%) of the assembly sequence was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes, and the Z and W sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-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 Apomyelois bistriatella specimen (ilApoBist1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.77, longitude -1.34) on 30 June 2021.The specimen was taken from woodland habitat by James Hammond (University of Oxford) using a light trap.The specimen was identified by the collector and preserved on dry ice.
The ilApoBist1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Whole organism tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.DNA was extracted from whole organism tissue of ilApoBist1 at the Wellcome Sanger Institute (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 Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from tissue of ilApoBist1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination as described previously (Howe et al., 2021).Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2022), which     The author reports the Z and W chromosomes but does not give details on how they were identified from the whole genome asssembly.The sex chromosomes should have half the coverage of the autosomes, but how were the Z and W distinguished from each other?On the basis of size or homology to other species with known sex chromosomes?
Even one brief sentence on this would be enough to clarify.

Kay Lucek
Biodiversity Genomics Laboratory, University of Neuchâtel, Neuchâtel, Switzerland The authors present the chromosome level genome assembly of the Heath Knot-horn, Apomyelois bistriatella.The assembly consists of 32 chromosomes including both sex chromosomes.The assembly is highly complete as revealed by the high BUSCO score but not fully phased.
Sequencing and genome assembly follow the current state of the art and use established methods.Overall, the presented assembly will be of great value to study genome architecture as well as genome size evolution in Lepidoptera.It states that "the genome will be annotated using available RNA-Seq data", however, according to Table 1 this data has not yet been deposited.

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?Partly Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Speciation 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 2 .
Figure 2. Genome assembly of Apomyelois bistriatella, ilApoBist1.1: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 389,571,851 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 (17,721,000 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (13,669,180 and 8,655,929 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/ilApoBist1.1/dataset/ ilApoBist1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Apomyelois bistriatella, ilApoBist1.1:Hi-C contact map of the ilApoBist1.1 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=Olwsrw1tR7mMGnnJQB8skA.

Table 3 . Software tools: versions and sources. Software tool Version 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 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
Reviewer Expertise: evolutionary genomics, sex chromosomes, Lepidoptera 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.
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