The genome sequence of the tachinid fly, Epicampocera succincta (Meigen, 1824) [version 1; peer review: 1 approved]

We present a genome assembly from an individual male Epicampocera succincta (a tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 398.1 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 21.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,733 protein coding genes.


Background
Epicampocera succincta (Meigen, 1824) is a common tachinid fly in central and southern England and Wales, with a few scattered records north of there and in Ireland. The overall appearance is of a black fly with light pruinosity and a slight gunmetal blue sheen, which makes it fairly unremarkable amongst many species that look similar (Tschorsnig & Herting, 1994). On closer examination, though, it has the unusual feature of a row of tiny hairs along the length of the silvery parafacial area and black, spoon-shaped palps (Belshaw, 1993). The primary hosts are butterflies of the genus Pieris but there are records from Hadena bicruris (Noctuidae) and in Europe from Evergestis forficalis (Pyralidae) and the non-British Ascotis selenania (Geometridae) (Belshaw, 1993;Ford & Shaw, 1991). The adults fly from May to late September, possibly in two broods, peaking in August. In 1993 Belshaw reported them as flying from July, but we have plenty of records from May and even late April suggesting that we now have a second brood in the UK (Belshaw, 1993;Ford et al., 2000).
The genome of Epicampocera succincta 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 Epicampocera succincta, based on one male specimen from Wytham Woods, Oxfordshire, England.

Genome sequence report
The genome was sequenced from one male Epicampocera succincta ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (51.77, -1.33). A total of 53-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 76 missing joins or mis-joins, reducing the scaffold number by 87.18%, and increasing the scaffold N50 by 107.04%.
The final assembly has a total length of 398.1 Mb in 10 sequence scaffolds with a scaffold N50 of 71.4 Mb (Table 1). Most (99.98%) 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 2- Figure 5; Table 2). The order and orientation of scaffolds on chromosome 1 in the region of 39.86-43.59 Mb is uncertain. 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/569040.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The idEpiSucc1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Thorax tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. 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 a Pacific Biosciences SEQUEL II (HiFi instrument. Hi-C data were also generated from head tissue of idEpiSucc2 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 as described previously (Howe et al., 2021). Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022). The mitochondrial genome was assembled using MitoHiFi       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 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.

Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
In the presented work, Steven Falk, Chris Raper and the DToL collective have sequenced, assembled and annotated the genome of a tachinid fly, Epicampocera succincta. The genome, containing 20,733 protein coding genes, is scaffolded to 7 chromosomes and the mitochondrial DNA molecule.
The produced genome is a nice contribution to the biodiversity genomics of Tachinidae, which with almost 8000 extant species are among the most diverse and rapidly evolving Dipteran families. The genome will prove to be useful in evolution and population genetics work among tachinids in particular and brachyceran flies in general.
The paper is well written and follows the standard protocols and techniques of the DToL genome production pipeline. I have only a couple of minor points: Background Epicampocera succincta is an important biocontrol agent of the large white (Pieris brassica), which can occasionally occur as a pest and might have been relevant to mention. Also based on the records in GBIF, the species occurs throughout the British Isles, which is noteworthy as the introduction mentioned England and Wales and "a few scattered records north of there" (=Scotland?).

Report
The species is fairly distinct and relatively easy for an expert to identify based on the characters presented in the background. While I trust the species determination, the Figure 1 presenting one of the specimens is barely adequate even for documentation purposes as the specimen itself is out of focus. As the specimen has been destroyed, this cannot be corrected anymore but photograph quality should be taken into better consideration in the future.
As the mtDNA sequence was obtained, it would be valuable to confirm the sequence of the Co1 DNA barcode region and provide the closest BIN match in BOLD.
No RNA sequencing was conducted?

Methods
For a future reference for specimen handling: Were the specimens identified before or after freezing? If before, was there need for immobilising the specimens or how were they investigated?

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