Abstract
We present a genome assembly from an individual male Thecophora atra (a Conopid fly; Arthropoda; Insecta; Diptera; Conopidae). The genome sequence is 354.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 30,620 protein coding genes.
Keywords: Thecophora atra, conopid fly, genome sequence, chromosomal, Diptera
Species taxonomy
Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Schizophora; Acalyptratae; Conopoidea; Conopidae; Myopinae; Thecophora; Thecophora atra (Fabricius, 1775) (NCBI:txid1219171).
Background
Thecophora atra (Fabricius, 1775) is a medium sized black fly from the family Conopidae, occasionally called thick-headed flies. It is one of three species from genus Thecophora Rondani, 1845 occurring in Britain ( Ransom et al., 2015; Whitehead, 2022). It differs from Thecophora fulvipes (Robineau-Desvoidy, 1830) by being slightly smaller in size ( T. atra is 4–7 mm, in contrast to 5–9 mm of T. fulvipes) and having scarcer dusting on the abdomen. The legs of T. atra are usually black with yellow “knees” (distal tip of the femora and proximal tip of the tibia) and a yellow basal half of the hind femora, while in T. fulvipes all the femora are entirely yellow or orange-brown (the hind one at least in basal two-thirds). The leg colouration is somewhat variable and some T. atra may have some yellow at the base or apex of front and/or mid femora ( Ransom et al., 2015; Smith, 1969).
Thecophora cinerascens (Meigen, 1804) was discovered in the Channel Islands in 2015 and in Wales in 2019, adding another species to the British list. Although similar in size and appearance to T. atra, the females of both species can be reliably separated by the shape of theca ( Ransom et al., 2015; Whitehead, 2022). Male T. atra and T. cinerascens are very difficult to separate. The specimen used for sequencing was confirmed as T. atra using DNA barcodes.
Thecophora atra is oviparous and its larvae are internal parasites of halictid bees. Usually, a single egg is laid in flight into a host’s abdomen. The white and smooth larva feeds on the insides of the abdomen during which time the host is active. The larva then becomes tapered anteriorly (in the third instar) and feeds on the contents of the thorax through the petiole resulting in the death of the host. Pupation occurs soon after, inside the host’s abdomen ( Smith, 1966).
The hosts recorded outside Britain include Halictus and Lasioglossum species. In Britain, T. atra has been observed around colonies of Lasioglossum morio and Halictus spp., but parasitism of these species has not been confirmed through rearing ( Baldock & Early, 2015; Smith, 1969).
The adults can be seen on flowers, particularly on ragwort Jacobaea spp. (= Senecio spp.), rough hawkbit Leontodon hispidus, devil’s-bit scabious Succisa pratensis (= Scabiosa succisa), water mint Mentha aquatica, hawkweed Hieracium spp., speedwells Veronica spp., common rock-rose Helianthemum nummularium and thistles ( Baldock & Early, 2015; Smith, 1969). Thecophora atra occurs on chalk, calcareous or basi-neutral habitats such as species-rich grasslands, and can also be found on or near the coast ( Baldock & Early, 2015; Ransom et al., 2015). Thecophora atra is widely distributed in Britain and Ireland, more common in southern Britain, scarcer in northern England, with few records from Scotland ( Ransom et al., 2015; Smith, 1969). T. atra is on the wing from May to October, peaking in August ( Baldock & Early, 2015; Smith, 1969).
The high-quality genome of a conopid fly Thecophora atra was sequenced based on one male specimen from Hartslock Nature Reserve. It will aid research on the taxonomy, phylogeny and biology of this and related taxa. The genome of T. atra 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.
Genome sequence report
The genome was sequenced from one male Thecophora atra ( Figure 1) collected from Hartslock Reserve, Oxfordshire (51.51, –1.11). A total of 44-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 misjoins and removed two haplotypic duplications, reducing the assembly length by 0.66% and the scaffold number by 52.17%, and increasing the scaffold N50 by 122%.
Figure 1. Photographs of the Thecophora atra (specimen ID NHMUK014444618, ToLID idTheAtra2) specimen used for genome sequencing.
A. The specimen in lateral view. B. The specimen in dorsal view. Photographs by Olga Sivell.
The final assembly has a total length of 354.2 Mb in 22 sequence scaffolds with a scaffold N50 of 94.1 Mb ( Table 1). Most (99.94%) of the assembly sequence was assigned to 5 chromosomal-level scaffolds, representing three autosomes and the X and Y sex chromosomes. The Y chromosome was identified based on read coverage against the Hi-C reads from a different specimen. 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.
Figure 2. Genome assembly of Thecophora atra, idTheAtra2.1: 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 354,246,487 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 (98,076,447 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (94,083,503 and 8,213,565 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/Thecophora%20atra/dataset/CALMKQ01/snail.
Figure 5. Genome assembly of Thecophora atra, idTheAtra2.1: Hi-C contact map of the idTheAtra2.1 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=LDkQ8LYLT9KdKtYbH37mvw.
Table 1. Genome data for Thecophora atra, idTheAtra2.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | idTheAtra2.1 | |
| Species | Thecophora atra | |
| Specimen | idTheAtra2 | |
| NCBI taxonomy ID | 1219171 | |
| BioProject | PRJEB51036 | |
| BioSample ID | SAMEA7849382 | |
| Isolate information | idTheAtra2: head (DNA sequencing)
idTheAtra3: thorax (Hi-C data) idTheAtra1: whole organism (RNA sequencing) |
|
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 65 | ≥ 50 |
| k-mer completeness | 100% | ≥ 95% |
| BUSCO ** | C:96.3%[S:95.2%,D:1.2%],
F:0.8%,M:2.9%,n:3,285 |
C ≥ 95% |
| Percentage of assembly mapped
to chromosomes |
99.94% | ≥ 95% |
| Sex chromosomes | X and Y chromosomes | localised homologous pairs |
| Organelles | Mitochondrial genome assembled | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR8978460 | |
| Hi-C Illumina | ERR8702824 | |
| PolyA RNA-Seq Illumina | ERR10123684 | |
| Genome assembly | ||
| Assembly accession | GCA_937620795.1 | |
| Accession of alternate haplotype | GCA_937641085.1 | |
| Span (Mb) | 354.2 | |
| Number of contigs | 94 | |
| Contig N50 length (Mb) | 7.7 | |
| Number of scaffolds | 22 | |
| Scaffold N50 length (Mb) | 94.1 | |
| Longest scaffold (Mb) | 98.1 | |
| Genome annotation | ||
| Number of protein-coding genes | 30,620 | |
| Number of gene transcripts | 31,353 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).
** BUSCO scores based on the diptera_odb10 BUSCO set using v5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Thecophora%20atra/dataset/CALMKQ01/busco.
Figure 3. Genome assembly of Thecophora atra, idTheAtra2.1: 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/Thecophora%20atra/dataset/CALMKQ01/blob.
Figure 4. Genome assembly of Thecophora atra, idTheAtra2.1: 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/Thecophora%20atra/dataset/CALMKQ01/cumulative.
Table 2. Chromosomal pseudomolecules in the genome assembly of Thecophora atra, idTheAtra2.
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| OW569397.1 | 1 | 98.08 | 38.0 |
| OW569399.1 | 2 | 74.24 | 36.5 |
| OW569401.1 | 3 | 42.38 | 37.5 |
| OW569398.1 | X | 94.08 | 38.5 |
| OW569400.1 | Y | 8.99 | 39.0 |
| OW569402.1 | MT | 0.02 | 21.0 |
The estimated Quality Value (QV) of the final assembly is 65 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 96.3% (single = 95.2%, duplicated = 1.2%), using the diptera_odb10 reference set ( n = 3,285).
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/1219171.
Genome annotation report
The Thecophora atra genome assembly (GCA_937620795.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Thecophora_atra_GCA_937620795.1/Info/Index). The resulting annotation includes 31,353 transcribed mRNAs from 30,620 protein-coding genes.
Methods
Sample acquisition and nucleic acid extraction
Thecophora atra specimens (idTheAtra2 and idTheAtra3 NHMUK014444821) were collected from Hartslock Nature Reserve, Oxfordshire, UK (latitude 51.51, longitude –1.11) on 2020-08-20 using an aerial net. The specimens were collected and identified by Ryan Mitchell (Natural History Museum) and preserved on dry ice.
The specimen used for RNA sequencing (specimen ID Ox000734, ToLID idTheAtra1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (51.766, –1.309) on 2020-08-03 by netting. This specimen was collected and identified by Steven Falk (independent researcher).
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The idTheAtra2 sample was weighed and dissected on dry. Head 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. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from whole organism tissue of idTheAtra1 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer’s instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit. Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from thorax tissue of idTheAtra3 using the Arimav2 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). One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes ( Garrison & Marth, 2012). 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., 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.
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, the k-mer completeness and QV consensus quality values were calculated in Merqury ( Rhie et al., 2020). This work was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.
Table 3 contains a list of relevant software tool versions and sources.
Table 3. Software tools: versions and sources.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 3.4.0 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| Hifiasm | 0.16.1-r375 | https://github.com/chhylp123/hifiasm |
| HiGlass | 1.11.6 | https://github.com/higlass/higlass |
| Merqury | MerquryFK | https://github.com/thegenemyers/MERQURY.FK |
| MitoHiFi | 2 | https://github.com/marcelauliano/MitoHiFi |
| PretextView | 0.2 | https://github.com/wtsi-hpag/PretextView |
| purge_dups | 1.2.3 | https://github.com/dfguan/purge_dups |
| sanger-tol/genomenote | v1.0 | https://github.com/sanger-tol/genomenote |
| sanger-tol/readmapping | 1.1.0 | https://github.com/sanger-tol/readmapping/tree/1.1.0 |
| YaHS | yahs-1.1.91eebc2 | https://github.com/c-zhou/yahs |
Genome annotation
The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Thecophora atra assembly (GCA_937620795.1) in Ensembl Rapid Release.
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 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
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 2 approved, 2 approved with reservations]
Data availability
European Nucleotide Archive: Thecophora atra. Accession number PRJEB51036; https://identifiers.org/ena.embl/PRJEB51036. ( Wellcome Sanger Institute, 2022)
The genome sequence is released openly for reuse. The Thecophora atra 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.
Author information
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4790042.
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4789928.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.
Members of the Wellcome Sanger Institute Tree of Life programme are listed here: https://doi.org/10.5281/zenodo.4783585.
Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
References
- Abdennur N, Mirny LA: Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Baldock DW, Early JP: Soldierflies, their allies and Conopidae of Surrey.Surrey Wildlife Trust,2015. [Google Scholar]
- Bernt M, Donath A, Jühling F, et al. : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–319. 10.1016/j.ympev.2012.08.023 [DOI] [PubMed] [Google Scholar]
- Brůna T, Hoff KJ, Lomsadze A, et al. : BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom Bioinform. 2021;3(1): lqaa108. 10.1093/nargab/lqaa108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R, Richards E, Rajan J, et al. : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Di Tommaso P, Chatzou M, Floden EW, et al. : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. 10.1038/nbt.3820 [DOI] [PubMed] [Google Scholar]
- Garrison E, Marth G: Haplotype-based variant detection from short-read sequencing. 2012; [Accessed 26 July 2023]. 10.48550/arXiv.1207.3907 [DOI] [Google Scholar]
- Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 10.1093/bioinformatics/btaa025 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harry E: PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps. 2022; Accessed 19 October 2022. Reference Source
- Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10(1): giaa153. 10.1093/gigascience/giaa153 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1): 125. 10.1186/s13059-018-1486-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Manni M, Berkeley MR, Seppey M, et al. : BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647–4654. 10.1093/molbev/msab199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ransom TM, Falk SJ, Clements DK: Thecophora cinerascens (Meigen) (Diptera, Conopidae) new to the British Isles from Jersey. Dipterist’s Digest. 2015;22:135–141. [Google Scholar]
- Rao SSP, Huntley MH, Durand NC, et al. : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–1680. 10.1016/j.cell.2014.11.021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, McCarthy SA, Fedrigo O, et al. : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737–746. 10.1038/s41586-021-03451-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, Walenz BP, Koren S, et al. : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1): 245. 10.1186/s13059-020-02134-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Simão FA, Waterhouse RM, Ioannidis P, et al. : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–3212. 10.1093/bioinformatics/btv351 [DOI] [PubMed] [Google Scholar]
- Smith KG: The larva of Thecophora occidensis, with comments upon the biology of Conopidae: Diptera. J Zool. 1966;149(3):263–276. 10.1111/j.1469-7998.1966.tb04048.x [DOI] [Google Scholar]
- Smith KGV: Diptera, Conopidae.In: Handbooks for the Identification of British Insects. 1969;3(a):1–19. [Google Scholar]
- Surana P, Muffato M, Qi G: sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a; Accessed 21 July 2023. 10.5281/zenodo.7755665 [DOI] [Google Scholar]
- Surana P, Muffato M, Sadasivan Baby C: sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b; Accessed 21 July 2023. Reference Source
- Uliano-Silva M, Ferreira JGRN, Krasheninnikova K, et al. : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023;24(1): 288. 10.1186/s12859-023-05385-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vasimuddin M, Misra S, Li H, et al. : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).IEEE,2019;314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Wellcome Sanger Institute: The genome sequence of a conopid fly, Thecophora atra (Fabricius, 1775). European Nucleotide Archive.[dataset], accession number PRJEB51036,2022.
- Whitehead PF: Thecophora cinerascens (Meigen, 1804)(Diptera, Conopidae) new to mainland Britain. Entomologist’s Gazette. 2022;73(1):55–57. 10.31184/G00138894.731.1816 [DOI] [Google Scholar]
- Zhou C, McCarthy SA, Durbin R: YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39(1): btac808. 10.1093/bioinformatics/btac808 [DOI] [PMC free article] [PubMed] [Google Scholar]