The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775)

We present a genome assembly from an individual male Hypsopygia costalis (the Gold Triangle; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 818 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,248 protein coding genes.


Background
Hypsopygia costalis (Fabricius, 1775) is a moth in the Pyralidae family, known as the Gold Triangle in the British Isles, and the Clover Hayworm in North America.Its British and Irish common name derives from the characteristic golden yellow triangular markings formed where the narrow fasciae broaden as they meet the costa.Within the British Isles, the moth is most often encountered in England and Wales, becoming scarcer as it moves north towards the extremity of its range in the Scottish Borders (Cubitt, 2021;Parsons & Davis, 2018).The species is apparently absent from Ireland, with only three records that may constitute accidental imports (Walsh et al., 2009).Globally, the moth occurs in Europe and eastern North America (GBIF Secretariat, 2021).
The larva feeds on dried vegetation, most notably hay made from clover or alfalfa, of which it can be a serious pest, thus earning it its North American common name (Goater et al., 1986;Parsons & Davis, 2018;Swenk, 1908).The species is also thought to feed on thatch and has even been reported feeding on vegetable matter within a squirrel's drey (Goater et al., 1986).Pupation occurs within an oval cocoon in the feeding locale (Parsons & Davis, 2018).The adult moth measures 18-22 mmin wingspan and is on the wing from July to November (Goater et al., 1986;Parsons & Davis, 2018).It is nocturnal, resting by day in thatch and hedgerows, or in the case of a hay infestation, can be found resting on the walls of barns (Goater et al., 1986;Swenk, 1908).The adult is attracted to light, and has also been reported at sugar (Swenk, 1908).
The genome of H. costalis 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 H. costalis, based on one male specimen from Wytham Woods, Berkshire, UK.

Genome sequence report
The genome was sequenced from one male H. costalis (Figure 1) collected from Wytham Woods, Berkshire, UK (latitude 51.77, longitude -1.34).A total of 50-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 38-fold coverage in 10X Genomics read clouds was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected seven missing or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 7.69%.
The final assembly has a total length of 817.7 Mb in 48 sequence scaffolds with a scaffold N50 of 28.9 Mb (Table 1).Most (99.91%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 98.8% (single 98.2%, duplicated 0.6%) using the OrthoDB v10 lepidoptera reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Genome annotation report
The GCA_937001555.1 genome assembly was annotated using the Ensembl rapid annotation pipeline (Table 1; https://rapid.ensembl.org/Hypsopygia_costalis_GCA_937001555.1/).The resulting annotation includes 19,419 transcripts from 19,248 protein-coding genes.longitude -1.34) using a light trap.The specimens were collected and identified by Douglas Boyes (University of Oxford) and snap-frozen on dry ice.

Sample acquisition and nucleic acid extraction
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilHypCost1 sample was weighed and dissected on dry ice.Whole organism tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 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 of 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 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 and 10X Genomics read cloud 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) and Illumina NovaSeq 6000 (10X) instruments.Hi-C data were also generated from ilHypCost2 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
The genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where relevant.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used to annotate the H. costalis genome assembly (GCA_937001555.1) in Ensembl Rapid Release.BRAKER2 performs automatic gene annotation as a draft annotation without transcriptomic data.We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Hypsopygia costalis, ilHypCost1.2: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 816,870,447 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest sequence present in the assembly (34,377,200 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 sequence lengths (28,834,930 and 20,016,790 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/Hypsopygia%20costalis/dataset/CAKZJR01/snail.

Figure 5 .
Figure 5. Genome assembly of Hypsopygia costalis, ilHypCost1.2:Hi-C contact map.Hi-C contact map of the ilHypCost1.2assembly, visualised using HiGlass.The female specimen lHypCost2 was used to generate the Hi-C library.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=TGGC-QK7QQujf69Q2nhz8g.

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.
https://doi.org/10.21956/wellcomeopenres.20785.r62215