The genome sequence of a tachinid fly, Tachina lurida (Fabricius, 1781)

We present a genome assembly from an individual female Tachina lurida (a tachinid fly; Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 899.2 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,127 protein coding genes.


Background
Tachina lurida (Diptera, Tachinidae) is a medium sized (9-12 mm) long tachinid fly. In older literature (van Emden, 1954) the species is referred to as Servillia lurida, but taxonomic revisions have reduced Servillia to a subgenus of Tachina (Chandler, 1998). Members of the subgenera Servillia Robineau-Desvoidy are characterised by a dense coat of long hairs. These long hairs can obscure the larger bristles on the body, and in the field the overall appearance of T.lurida is that of a pale brown, very 'furry' fly. The body is mostly dark, with orange patches at the sides of the upper segments of the abdomen and the apex of the scutellum.
The larvae are solitary internal parasites of a range of treefeeding Lepidoptera larvae, mostly from the family Noctuidae including the Common Quaker Orthosia stabilis (Belshaw, 1993) and the Small Quaker Orthosia cruda. Other occasionally recorded hosts include Sphingidae (Van Emden, 1954) and Lasiocampidae (Tschorsnig & Herting, 1994). Eggs are laid on the host foodplant in the vicinity of the host and the fly pupates in the empty host integument.
In Britain, Tachina lurida is a widespread species, most often recorded from woodland margins. The majority of the records are from the south-east of Britain, with scattered records extending northwards and westwards into Wales and southern Scotland. There are no records from Ireland. The species is single brooded, with the adults on the wing between later March or early April through until June.

Genome sequence report
The genome was sequenced from one female Tachina lurida ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (51.76, -1.34). A total of 23-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 158 missing joins or mis-joins and removed 6 haplotypic duplications, reducing the assembly length by 0.31% and the scaffold number by 71.72%, and increasing the scaffold N50 by 80.12%.
The final assembly has a total length of 899.2 Mb in 41 sequence scaffolds with a scaffold N50 of 167.3 Mb (Table 1). Most (99.94%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds, representing 5 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). 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/631329.

Sample acquisition and nucleic acid extraction
A female Tachina lurida (specimen ID Ox001286, individual idTacLuri1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude -1.34) on 2021-04-23 using a net. The specimen was collected and identified by Steven Falk (independent researcher), and was then snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The idTacLuri1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Thorax 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    Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from head tissue of idTacLuri1 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  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 (Uliano-Silva et al., 2022), 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.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Tachina lurida assembly (GCA_944452675.1). Annotation was created primarily through alignment of transcriptomic data to the genome, with   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 The genome sequence is released openly for reuse. The Tachina lurida 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. Raw data and assembly accession identifiers are reported in Table 1.