The genome sequence of the Sulphur Tubic, Esperia sulphurella (Fabricius, 1775)

We present a genome assembly from an individual male Esperia sulphurella (the Sulphur Tubic; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.2 kilobases in length.


Background
Esperia sulphurella is a small moth in the family Oecophoridae sometimes called the 'Sulphur Tubic'.Although primarily a day-flying species, the adults will also come to light at night.In the UK the moth is widely distributed but probably under-recorded due to its small size (12-16 mm wingspan).The moth is also common in the Netherlands and Belgium and there are scattered records from across Europe, plus some records from the west coast of the United States where it is likely an imported species (GBIF Secretariat, 2022;Powell, 1968;Powell & Opler, 1996).E. sulphurella can be common at some woodland and garden sites in southern England and Wales where dead wood is present, and the adults can be seen in April and May in sunny patches (NBN Atlas, 2022).The moth has distinctive wing markings comprising a rich brown ground colour flecked with bright yellow scales, many of which are grouped to form a triangle at the trailing edge of each forewing forming a diamond shape when viewed from above.Females also have a pronounced yellow streak along the wing (Asher, 2013).
The moth has one generation per year, with the adults laying eggs in crevices on bark.The larvae live in silken tubes inside dry rotting wood, including dead trunks of coniferous and deciduous trees, stacked wood piles and fence posts, but never close to where the wood is touching wet ground (Harper et al., 2002).The larvae may eat rotting wood and associated fungi.
A genome sequence of E. sulphurella will be useful in analyses of molecular adaptations to feeding on wood and fungus, and as part of wider comparative studies into genome evolution in the Lepidoptera.

Genome sequence report
The genome was sequenced from one male Esperia sulphurella (Figure 1) collected from Wallingford, Oxfordshire (latitude 51.60, longitude -1.14).A total of 62-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 22 missing or mis-joins and removed six haplotypic duplications, reducing the assembly length by 0.21% and the scaffold number by 12.5%.
The final assembly has a total length of 453.2 Mb in 35 sequence scaffolds with a scaffold N50 of 16.4 Mb (Table 1).Most (99.97%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 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 98.1% (single 97.5%, duplicated 0.7%) 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 nucleic acid extraction
A male Esperia sulphurella (specimen ToLID ilEspSulp1, specimen Ox001336) was collected in Wallingford, Oxfordshire (biological vice-county: Berkshire) (latitude 51.60, longitude -1.14) on 14 May 2021.The specimen was taken from a garden habitat by Peter Holland (University of Oxford) using a light trap.The specimen was identified as a male on the basis of wing markings by Peter Holland, and was frozen at -80°C.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEspSulp1 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.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.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 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 ilEspSulp1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with  environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.This report is for a reference quality genome assembly of the Sulphur Tubic moth with sound methodology and presentation of final results.The authors have successfully generated the complete assembly with 29 autosomes, the Z sex chromosome and mitochondria.I look forward to tracking this assembly as the official gene set is produced.

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, computational biology, evolution 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.

Maurijn van der Zee
Institute of Biology, Leiden University, Sylviusweg, Leiden, The Netherlands Peter Holland provides the genome sequence of the Sulphur Tubic moth.Judging from the description, the geome is of high quality, as the 35 scaffolds nearly represent the number of chromosomes (30), and the BUSCO score practically suggest completion.The manual curation particularly improved the assembly.Thus, this will be a valubale contribution to the community.Note that I could download the genomic and transcriptomic fasq files from the site, but not the actual assembly (or did I overlook something?).I trust that this will be made easily available.
Is the rationale for creating the dataset(s) 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?No Competing Interests: No competing interests were disclosed.
Reviewer Expertise: evo-devo, insects, comparative 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 Esperia sulphurella, ilEspSulp1.1: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 453,222,902 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 (26,432,394 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (16,376,554 and 10,956,773 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/ilEspSulp1.1/dataset/CAMTYV01/snail.

Figure 3 .
Figure 3. Genome assembly of Esperia sulphurella, ilEspSulp1.1:GC coverage.BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilEspSulp1.1/dataset/CAMTYV01/blob.

Figure 4 .
Figure 4. Genome assembly of Esperia sulphurella, ilEspSulp1.1:cumulative sequence.BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilEspSulp1.1/dataset/ CAMTYV01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Esperia sulphurella, ilEspSulp1.1:Hi-C contact map.Hi-C contact map of the ilEspSulp1.1 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=b_dgwdvFRF-QNCmAPPStBw.

INSDC accession Chromosome Size (Mb) GC%
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.

Table 3 . Software tools and versions used. Software tool Version Source
The genome sequence is released openly for reuse.The Esperia sulphurella genome sequencing initiative is part of the Darwin Tree of Life (DToL) project.All raw sequence data and the assembly have been deposited in INSDC databases.The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute.Raw data and assembly accession identifiers are reported in Table1.

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.

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.Cohen Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center,Agricultural Research Service, United States Department of Agriculture, College Station, TX, USA https://doi.org/10.21956/wellcomeopenres.21294.r70224© 2023 Cohen Z.