The genome sequence of the white ermine, Spilosoma lubricipeda Linnaeus 1758

We present a genome assembly from an individual male Spilosoma lubricipeda (the white ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 587 megabases in span. The majority of the assembly is scaffolded into 30 chromosomal pseudomolecules, with the Z sex chromosome assembled.


Introduction
Spilosoma lubricipeda (White ermine) is found across much of Eurasia but has decreased in abundance significantly in the UK in recent decades, with the cause(s) being unknown (Fox et al., 2013) (Prescott et al., 2019 The genome of S. lubricipeda was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all of the named eukaryotic species in the Atlantic Archipelago of Britain and Ireland. Here we present a chromosomally complete genome sequence for S. lubricipeda, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a single male S. lubricipeda collected from Wytham Woods, Oxfordshire, UK (latitude 51.768, longitude -1.337). A total of 39-fold coverage in Pacific Biosciences single-molecule long reads and 43-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 22 missing/misjoins and removed 2 haplotypic duplications, reducing the assembly length by 0.09% and increasing the scaffold number by 3.70%. The final assembly has a total length of 587 Mb in 37 sequence scaffolds with a scaffold N50 of 21 Mb (Table 1). Of the assembly sequence, 99.98% was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes (numbered by sequence length), and the Z sex chromosome (Figure 1- Figure 4; Table 2). The assembly has a BUSCO (Simão et al., 2015) v5.1.2 completeness of 98.8% 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.

Methods
A single male S. lubricipeda was collected from Wytham Woods, Oxfordshire, UK (latitude 51.768, longitude -1.337) by Douglas Boyes, University of Oxford using a light trap. The specimens were snap-frozen in dry ice using a CoolRack before transferring to the Wellcome Sanger Institute (WSI).
DNA was extracted at the Tree of Life laboratory, WSI. The ilSpiLubr1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Abdomen tissue was disrupted to a fine powder using a Biomasher tissue homogeniser. 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 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.       The genome sequence is released openly for reuse. The S. lubricipeda 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 and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.  1. Is the collection record shared somewhere (GPS coordinates, etc.)? If not, it would be good to include. I couldn't find it on ENA, but it's possible this is due to my own unfamiliarity with the ENA.

INSDC accession
2. The paper mentions that the PacBio HiFi library was prepared according to manufacturer instructions, but the exact protocol used was missing (standard protocol/low input protocol/ultralow protocol).
3. For the polishing step were all Chromium reads mapped to the haploid or the diploid assembly? In my own work, I've noticed that in areas of substantial heterozygosity, short reads often do a poor job of polishing due to inaccurate mapping. In my experience, at least, this is partly alleviated by using a diploid genome assembly or by attempting to phase reads before the polishing step.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound? Partly

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? Yes The S. lubricipeda assembly is 587 Mb long. Although the S. lubricipeda genome size is not known, some comparison with a genome size inferred from k-mers would be nice. Anyway, the assembly length seems to be close to a genome size of its congener, S. virginica (626 Mb according to www.genomesize.com). 99.98% of sequence was assigned to 30 chromosome-level scaffolds, which is interesting as Robinson (1971, Lepidoptera genetics) 1 provides chromosome number n=31 for this species citing two independent references. The Z chromosome is surprisingly large in S. lubricipeda. The karyotype n=31 is ancestral in Lepidoptera and comparison with genome of some other species with n=31 such as Plutella xylostella, Spodoptera litura, or Melitaea cinxia could reveal fusion between the Z chromosome and an autosome which occurred in the sampled S. lubricipeda population. The authors should address the above mentioned in their genome sequence report.
The method section describes the pipeline but not the parameters used. For better reproducibility, parameters used for individual processing and assembly steps should be specified.
Description of the software version used is not consistent throughout the paper. At the Genome sequence report section, you identify the version of the BUSCO score/program with v5.1.2 but then the rest of the software tools do not have the version next to them but on Table 3.

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There are missing citations in the text. Methods section, 4th paragraph. HiGlass and Pretext.
○ Also, in the Methods section, 4th paragraph, on the sentence before last: "The genome was analyzed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020)." -Although I understand the context of the sentence, the flow of the paragraphs seems to indicate that this sentence refers to the mitochondrial assembly which is incorrect.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound? Yes