The genome sequence of the rosy rustic, Hydraecia micacea (Esper, 1789)

We present a genome assembly from an individual female Hydraecia micacea (the rosy rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 562 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 16.3 kilobases in length.


Background
The Rosy Rustic Moth (Hydraecia micacea) is found across the northern hemisphere and was introduced into North America in the early 1900s (Šedivý et al., 2010).The species is classed as vulnerable in the UK using International Union for Conservation of Nature (IUCN) criteria (Conrad et al., 2006).Hydraecia micacea is mostly found in wetlands and has one generation per year with its flying period occurring approximately from mid-July until October (Weihrauch, 2020).The species feeds on approximately 50 different plant species and is a damaging pest to weeds and several crop species including potatoes, cereals and hops due to the moth's stem boring larvae (Gryndler et al., 2008;Šedivý et al., 2010).The genome of this species will give an insight into H. micacea's herbivory habits allowing for more targeted pest control methods (You et al., 2013).

Genome sequence report
The genome was sequenced from one female H. micacea (Figure 1) collected from Wytham Woods, Oxfordshire (Biological vice-county: Berkshire), UK (latitude 51.772, longitude -1.338).A total of 30-fold coverage in Pacific Biosciences single-molecule long reads and 79-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 11 missing/misjoins, reducing the scaffold number by 18.60%, and increasing the scaffold N50 by 0.29%.
The final assembly has a total length of 562 Mb in 35 sequence scaffolds with a scaffold N50 of 18.9 Mb (Table 1).The majority of the assembly sequence (99.98%) was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the W and Z sex chromosomes (Figure 2-Figure 5; Table 2).The assembly has a BUSCO v5.2.2 (Manni et al., 2021) completeness of 99.1% (single 98.6%, duplicated 0.5%) using the lepidoptera_odb10 reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and DNA extraction
A single female H. micacea (ilHydMica1) was collected from Wytham Woods, Oxfordshire (Biological vice-county: Berkshire), UK (latitude 51.772, longitude -1.338) by Douglas  Boyes, UKCEH, using a light trap in woodland.The sample was identified by the same individual, and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute.The ilHydMica1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.
Thorax tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a

Simon H Martin
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK The report describes a chromosomal assembly for the rosy rustic moth.The approaches used are state of the art, and the resulting assembly is of high quality.I have no scientific concerns with the report.
I spotted one factual error: Table 1 reports that the longest scaffold is 22 Mb, but it should be 27 Mb (Z chromosome).
Note that in some places Latin names are not italicised.

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: Evolutionary 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.
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 and annotation, comparative genomics, Lepidoptera 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 Hydraecia micacea, ilHydMica1.1: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 562,441,436 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 (26,946,823 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 chromosome lengths (18,862,954 and 12,891,245 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/ilHydMica1.1/dataset/CAJZBC01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Hydraecia micacea, ilHydMica1.1:Hi-C contact map.Hi-C contact map of the ilHydMica1.1 assembly, visualised in HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this map is available here.
Table 3 contains a list of all software tool versions used, where appropriate.
Ethics/compliance issuesThe 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.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the

Table 3 . Software tools used.
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.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. legal