The genome sequence of a barkfly, Mesopsocus fuscifrons Meinander, 1966

We present a genome assembly from an individual female Mesopsocus fuscifrons (barkfly; Arthropoda; Insecta; Psocodea; Mesopsocidae). The genome sequence is 184.3 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.13 kilobases in length.


Background
Mesopsocus fuscifrons is a large, 3.5-5.0mm long, barkfly (Psocodea: 'Psocoptera') that can be recognised by its very dark frons and distinctive eye pattern (Lienhard, 1998).The wings are fully formed in males, but reduced to vestigial wing buds in females.Female M. fuscifrons also have dark rings near the base of the tibiae that are characteristic of this species.The eye pattern can be described as a dark chevron that lies horizontally across the eye.In practice the eyes appear dark with a paler grey line running horizontally across their middle.Either interpretation is clearly different from the eyes of other British Mesopsocus, which can be identified using New (2005).
Mesopsocus fuscifrons is a recent addition to the British fauna with a population in the Wildlife Garden of the Natural History Museum in South Kensington (McCarter et al., 2021).Specimens captured in a Malaise trap in the summer of 2013 are the earliest British records we are aware of.This species has also been found at three sites in Richmond and Ham (Cook, 2023), and undoubtedly occurs elsewhere in the Greater London area.
This barkfly is a Mediterranean species known from Morocco, Algeria, France, Italy, Macedonia and Greece (Lienhard, 1998) that has expanded its range into northern Europe in the past decade.Mesopsocus fuscifrons is now recorded in Germany, northern France, Belgium, the Netherlands and Denmark as well as the UK (Schuch et al., 2021).There were also records from southern Sweden in 2006 but it is not clear if a population persists there (Svensson & Hall, 2010).
Mesopsocus fuscifrons has been found on a wide variety of broadleaved trees and shrubs that may or may not have lichens growing on the bark (Cook, 2023;Schuch et al., 2021).Lienhard (1998) also reports M. fuscifrons living on conifers.Across its geographic range M. fuscifrons adults may be found in any month of the year, though are more likely to be seen from May to October (Schuch et al., 2021).British records so far have been made from May to August (Cook, 2023).
A single female observed on the trunk of a young ash tree (Fraxinus excelsior) in the NHM Wildlife Garden was captured and submitted to the Darwin Tree of Life project on 8 June 2021.It has been suggested that Mesopsocus fuscifrons may be synonymous with M. ypsilon Ball, 1937, a species known from Morocco and Greece (Lienhard, 1998).The publication of this genome sequence will help to answer this question.

Genome sequence report
The genome was sequenced from one female Mesopsocus fuscifrons (NHMUK014043153, Figure 1) collected from Natural History Museum Wildlife Garden, England (51.5, -0.18).A total of 93-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 204 missing joins or mis-joins and removed 106 haplotypic duplications, reducing the assembly length by 4.60% and the scaffold number by 75.29%, and increasing the scaffold N50 by 13.37%.
The final assembly has a total length of 184.3 Mb in 20 sequence scaffolds with a scaffold N50 of 21.7 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.9%) of the assembly sequence was assigned to 9 chromosomal-level scaffolds, representing 9 autosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Sex chromosomes were not identified due to the lack of comparators within this order.Psocodea have multiple sex determination mechanisms (Hodson et al., 2017).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, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/ 2866285.on dry ice (Jay et al., 2023).Tissue from the whole organism was homogenised using a PowerMasher II tissue disruptor (Denton et al., 2023a).

Sample acquisition and nucleic acid extraction
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol (Oatley et al., 2023).HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31 (Bates et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation (Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.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.
Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory are publicly available on protocols.io(Denton et al., 2023b).

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 a Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from remaining tissue of iuMesFusc1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and    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.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 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 This study reports a high-quality genome assembly of barkfly at the chromosome level.
The rationale for why this study is reported and the dataset is created is clearly described.
The protocol described here is reasonable.However, if some details in sections of the genome assembly and the sample acquisition and DNA extraction are provided, the article would be improved.This is a minor comment that does not affect the approval.See the below for the detailed comments.
It is mentioned that the remaining tissue was used for HiC data after PacBio Hifi sequencing.Here, it is not described which tissues were used for PacBio Hifi and HiC sequencing.For genome assembly, it would be better to show which parameters are exactly used in each software program.
Can the Hi-C contact map show the contigs assembled into scaffolds in the figure?I think that this would help to assess how the initial assembly (contig-level) contribute to the scaffolded assembly.

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.
1.The total size of genome assembly is matching genome size determined by experimental methods like flow cytometry?If there is no data on genome size estimation, the genome size of the assembly is close to those of their relative species?
2. The author present 9 chromosomal-level scaffolds.Are the numbers close and reliable to those estimated from the number of chromosomes in closely related species?
3. Is the DNA for the sequencing derived from the whole body?
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: Genomics, Omics analysis 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 Mesopsocus fuscifrons, iuMesFusc1.1: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 184,352,988 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 (24,526,141 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (21,655,844 and 16,975,629 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 insecta_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CATLKH01/dataset/CATLKH01/snail.
iuMesFusc1) was observed on the trunk of a young ash tree in the Natural History Museum Wildlife Garden, England, UK (latitude 51.5, longitude -0.18) on 2021-06-08.The specimen was collected and identified by Duncan Sivell (Natural History Museum) and then dry frozen at -80 °C.The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.The sample was prepared in the WSI Tree of Life Core laboratory: the iuMesFusc1 sample was weighed and dissected

Figure 3 .
Figure 3. Genome assembly of Mesopsocus fuscifrons, iuMesFusc1.1: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/CATLKH01/dataset/CATLKH01/blob.

Figure 4 .
Figure 4. Genome assembly of Mesopsocus fuscifrons, iuMesFusc1.1: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/CATLKH01/dataset/CATLKH01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Mesopsocus fuscifrons, iuMesFusc1.1:Hi-C contact map of the iuMesFusc1.1 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=I7ipiU4sRtSk_uJrqsXM3Q.

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Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).

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.