The genome sequence of the centipede Strigamia acuminata (Leach, 1816)

We present a genome assembly from an individual male Strigamia acuminata (centipede; Arthropoda; Chilopoda; Geophilomorpha; Geophilidae; Linotaeniinae). The genome sequence is 237.5 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 15.07 kilobases in length.


Background
Strigamia acuminata is a western Palaearctic species distributed throughout most of continental Europe, from the Iberian Peninsula to the Caucasus and Volga basin, as well as Sicily, Crete and Great Britain (Bonato et al., 2012;Bonato et al., 2016;Bonato et al., 2023).Integrative taxonomy suggests that European populations of S. acuminata form a complex of at least two species (Bonato et al., 2023).In the UK, S. acuminata is known only from England and Wales, the largest numbers of records being from the southeast and east of England.The following occurrence data are summarised from Barber (2022).It is usually an inland species although some coastal records are known.It is collected throughout the year but has a patchy and unpredictable occurrence.Records are overwhelmingly in rural sites, with only a few urban occurrences.In Britain, as in Europe, S. acuminata is most common in deciduous woodland, and is less frequently found in mixed woodland and wetland.Its most typical microsites are under dead wood or in leaf litter.Most collections are from lowland sites (<200 m), but it has been found at up to 1,013 m in Snowdonia, north Wales.
Like the other two species of Strigamia in the UK, S. acuminata is distinguished in the field from most other British Geophilomorpha by its reddish colouration.Adults reach a body length of 30 mm in England and Wales but up to 40 mm in some European populations.A leg number of 37 to 41 pairs (versus 47 or more pairs) provides the simplest basis for its distinction from the other two British congeners, S. crassipes and S. maritima (Barber, 2008).Males have 37 or 39 leg pairs and females 41 in the UK; in other parts of the geographic range 39-43 pairs encompass the variation (Bonato et al., 2023).As in other congeners, the ultimate legs of females are slender and those of males swollen.In Germany, S. acuminata has been observed to group feed on the millipede Julus (Weil, 1958).
The genome of Strigamia acuminata 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 Strigamia acuminata, based on one adult male specimen from Bookham Common, Surrey.The genome is of interest for comparison with the most comprehensively annotated centipede genome, and the first to be sequenced, the closely related S. maritima (Chipman et al., 2014), which inhabits the littoral zone rather than woodland.

Genome sequence report
The genome was sequenced from one adult male Strigamia acuminata (Figure 1) collected from Bookham Common, Leatherhead,England (51.29,.A total of 98-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 99 missing joins or mis-joins and removed 23 haplotypic duplications, reducing the assembly length by 1.68% and the scaffold number by 27.06%, and increasing the scaffold N50 by 48.44%. The final assembly has a total length of 237.5 Mb in 158 sequence scaffolds with a scaffold N50 of 19.3 Mb (Table 1).Most (94.83%) of the assembly sequence was assigned to 11 chromosomal-level scaffolds, representing 9 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size  (Figure 2-Figure 5; Table 2).X and Y chromosomes in this genus are reported to be homomorphic (Green et al., 2016).In this assembly, SUPER_X and SUPER_Y both have half coverage.Y was determined based on the absence of BUSCO genes (arthropoda-odb10 gene set).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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/1255758.

Sample acquisition and nucleic acid extraction
An adult male Strigamia acuminata (specimen ID NHMUK014449029, ToLID qcStrAcum1) was collected from Bookham Common, Leatherhead, England, UK (latitude 51.29, longitude-0.38)on 2021-04-20.The specimen was collected by Gregory Edgecombe and Duncan Sivell (both Natural History Museum) and identified by Gregory Edgecombe, and was then preserved in 70% ethanol.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The qcStrAcum1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Somatic 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.
Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The 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', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal 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.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use (Kerpedjiev et al., 2018) and Pretext (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi (Uliano- Silva et al., 2023), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Maurijn van der Zee
Institute of Biology, Leiden University, Sylviusweg, Leiden, The Netherlands A pretty complete genome of the shorter red centipede Data are well described, are accessible, and could be downloaded.It is not entirely clear how the 158 scaffolds were assigned to 11 chromosomes, but I guess this was mainly done using the HiC data.It is of course great that these HiC data are available.This high quality genome is a valuable supplement to the Strigamia maritima genome, and a useful contribution to the scientific community.

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: Insect evo-devo, comparative genomics, evolve-and-resequence 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.

Jerome H.L Hui
Chinese University of Hong Kong, Hong Kong, China This is an excellent genomic resource!Here, Edgecombe and colleagues report the genome sequence of centipede Strigamia acuminata (Leach, 1816).This species is widely recorded in England and Wales.To date, genomic resources for myriapods including centipedes are generally scarce when comparing to other arthropods such as insects and crustaceans.Molecular data of this species are also scarce prior to this report, and are mainly confined to COI sequences deposited to the NCBI database.One great achievement that I personally highly appreciate is that this is the first report of the X and Y chromosomal sequences in centipede!This new genome resource will be very useful for further studies, such as understanding their evolutionary relationships with other arthropods.
In terms of quality, this genome resource is in also excellent judging from the summary statistics, with high BUSCO numbers, high sequence continuity (scaffold N50), and majority of sequences contained on the 11 pseudochromosomes (i.e. 9 autosomes + X + Y) (plus mitochondrion).To sum up, this is an outstanding and valuable contribution.

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: I have published with Peter Holland more than three years ago, and confirm that this potential conflict of interest did not affect my ability to write an objective and unbiased review of the article.
Reviewer Expertise: Genomics, evolution, invertebrates 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 Strigamia acuminata, qcStrAcum1.1: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 237,534,282 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 (66,985,994 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (19,347,077 and 9,836,499 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 arthropoda_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/qcStrAcum1.1/dataset/CASHSZ01/snail.

Figure 3 .
Figure 3. Genome assembly of Strigamia acuminata, qcStrAcum1.1: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/qcStrAcum1.1/dataset/CASHSZ01/blob.

Figure 4 .
Figure 4. Genome assembly of Strigamia acuminata, qcStrAcum1.1: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/qcStrAcum1.1/dataset/CASHSZ01/ cumulative.

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? Partly 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.
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.