The genome sequence of a tachinid fly, Linnaemya tessellans (Robineau-Desvoidy, 1830)

We present a genome assembly from one male Linnaemya tessellans (tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 709.9 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.


Background
Linnaemya tessellans (Diptera, Tachinidae) is a medium sized Tachinid fly.In older literature (Van Emden, 1954) the species is referred to as Linnaemyia pudica.Adults are dark, bristly flies with lines of pale dusting on the thorax.Careful examination is needed to separate L. tesselans from other similar closely related species such as Linnaemya rossica and Linnaemya pica (Raper, 2014).
Host details are limited.The larvae of other members of the genus are internal parasitoids of various Noctuid moth species, and it is likely that L. tesselans will have a similar host preference.Belshaw (1993) cites a "questionable record" from the Setaceous Hebrew Character Xestia c-nigrum, and Tschorsnig and Herting (1994) cite the same host species (as Amathes c-nigrum).
Linnaemya tessellans is sparingly recorded from the London region and the south-east of Britain, with occasional records north to Lincolnshire and south into Dorset.There are no records from Ireland.Adults are on the wing from early May until early October.The species is double brooded, with the peak of the spring brood in late May, followed by a large summer brood that reaches a peak in mid-August.
Here we present a chromosomal-level genome sequence for Linnaemya tessellans, sequenced as part of the Darwin Tree of Life Project.

Genome sequence report
The genome was sequenced from a male Linnaemya tessellans (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 50-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 46 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the scaffold number by 34.55%, and increasing the scaffold N50 by 23.97%. The final assembly has a total length of 709.9 Mb in 35 sequence scaffolds with a scaffold N50 of 125.2 Mb (Table 1).The snail plot 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 (99.08%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds, representing 5 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Sex chromosome assignment was guided by synteny to Tachina fera (GCA_905220375.1)(Nash et al., 2022).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.
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.In sample preparation, the idLinTess1 sample was weighed and dissected on dry ice (Jay et al., 2023).Tissue from the thorax was homogenised using a PowerMasher II tissue disruptor (Denton et al., 2023a).
HMW DNA was extracted using the Automated MagAttract v1 protocol (Sheerin et al., 2023).DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30 (Todorovic 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

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 A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics,     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

James B. Whitfield
University of Illinois at Urbana-Champaign, Champaign, IL, USA This manuscript describes the sequencing and assembly results for the (rather large, for a fly) genome of Linnaemya tesselans, a tachind fly.The genomic methods employed appear to be relatively state of the art, and a reasonable quality chromosomal level assembled genome has resulted.The genome has the potential to be highly useful for comparative studies of Diptera genomes, as it comes from a large and biologically interesting family of flies.
The "Background" part of the manuscript presents a rather matter-of-fact outline of what is known of the fly, and that appears to be relatively little.It is not clear why this fly was chosen for genomic study.Does it represent a particularly interesting lineage of tachinids for comparative biological study?Given that it is not well known, how will the genome be used to leverage insights into the group and its biology?In other words, more detail is needed in the introduction so that users will have some idea how to effectively use the information in the paper.
Otherwise, it is a straightforward genome report with little to criticize.

Is the rationale for creating the dataset(s) clearly described? No
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: Systematics, ecology and evolution of parasitoid wasps, comparative genomics of wasps and their symbiotic viruses.
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 Linnaemya tessellans, idLinTess1.1:metrics.The BlobToolKit snail plot 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 709,888,043 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 (171,573,740 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (125,158,878 and 104,166,244 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 diptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idLinTess1_1/dataset/idLinTess1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Linnaemya tessellans, idLinTess1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idLinTess1_1/dataset/idLinTess1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Linnaemya tessellans, idLinTess1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idLinTess1_1/dataset/idLinTess1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Linnaemya tessellans, idLinTess1.1:Hi-C contact map of the idLinTess1.1 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=QI8WhrWIQ4yef688QWCk-w.

:
Proposed standards and metrics for defining genome assembly quality" from Rhie et al. (2021).
the Qubit RNA Broad-Range Assay kit.Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io(Dentonetal., 2023b).

Table 3
contains a list of relevant software tool versions and sources.

Table 2 . Chromosomal pseudomolecules in the genome assembly of Linnaemya tessellans, idLinTess1. INSDC accession Chromosome Length (Mb) GC%
Wellcome Sanger Institute -Legal and GovernanceThe 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.

Table 3 . Software tools: versions and sources. Software tool Version 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.
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.