The genome sequence of the hoverfly, Epistrophella euchroma (Kowarz, 1885)
Steven Falk, Katie J. Woodcock, Chufei Tang, Sven Geibel
TL;DR
This paper provides the genome sequence of the hoverfly Epistrophella euchroma, including its sex chromosomes and mitochondrial genome.
Contribution
The novel contribution is the first genome assembly for Epistrophella euchroma, including chromosomal scaffolding and mitochondrial sequence.
Findings
The genome assembly spans 523.3 megabases and is scaffolded into 6 chromosomal pseudomolecules.
The mitochondrial genome is 17.24 kilobases in length and has been fully assembled.
Abstract
We present a genome assembly from an individual male Epistrophella euchroma (hoverfly, Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 523.3 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5| Project accession data | ||
|---|---|---|
| Assembly identifier | idEpiEuco1.1 | |
| Species |
| |
| Specimen | idEpiEuco1 | |
| NCBI taxonomy ID | 414814 | |
| BioProject | PRJEB54061 | |
| BioSample ID | SAMEA10978739 | |
| Isolate information | idEpiEuco1, male: whole organism (DNA sequencing and Hi-C
| |
| Assembly metrics
|
| |
| Consensus quality (QV) | 63.2 |
|
|
| 100% |
|
| BUSCO
| C:96.5%[S:95.9%,D:0.6%],F:0.8%,
|
|
| Percentage of assembly
| 99.99% |
|
| Sex chromosomes | X and Y chromosomes |
|
| Organelles | Mitochondrial genome
|
|
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR9924617 | |
| Hi-C Illumina | ERR9930692 | |
| Genome assembly | ||
| Assembly accession | GCA_947049315.1 | |
|
| GCA_947049305.1 | |
| Span (Mb) | 523.3 | |
| Number of contigs | 88 | |
| Contig N50 length (Mb) | 12.1 | |
| Number of scaffolds | 6 | |
| Scaffold N50 length (Mb) | 160.7 | |
| Longest scaffold (Mb) | 160.8 | |
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| 1 | 160.76 | 33.0 | |
| 2 | 160.67 | 33.0 | |
| 3 | 125.37 | 32.5 | |
| 4 | 66.03 | 32.5 | |
| X | 8.84 | 33.0 | |
| Y | 1.63 | 34.5 | |
| MT | 0.02 | 18.0 |
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.1.5 |
|
| BUSCO | 5.3.2 |
|
| Hifiasm | 0.16.1-r375 |
|
| HiGlass | 1.11.6 |
|
| Merqury | MerquryFK |
|
| MitoHiFi | 2 |
|
| PretextView | 0.2 |
|
| purge_dups | 1.2.3 |
|
| sanger-tol/genomenote | v1.0 |
|
| sanger-tol/readmapping | 1.1.0 |
|
| YaHS | yahs-1.1.91eebc2 |
|
- —Wellcome Trust
- —Wellcome Trust
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsDiptera species taxonomy and behavior · Insect symbiosis and bacterial influences · Fossil Insects in Amber
Species taxonomy
Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Aschiza; Syrphoidea; Syrphidae; Syrphinae; Syrphini; Epistrophella; Epistrophella euchroma (Kowarz, 1885) (NCBI:txid414814).
Background
The European hoverfly species Epistrophella euchroma (Kowarz, 1885), sometimes placed within the Meligramma or Epistrophe genus, is a scarce forest-associated hoverfly species encountered predominantly in the southern UK ( Ball & Morris, 2000; van Veen, 2010). Limited UK records of this species are available with the majority of these coming from Surrey and Hampshire in the months of May and June ( Ball & Morris, 2000; Ball & Morris, 2015; Dipterists Forum, 2020), though in 2019 an uncharacteristic rise in numbers was reported which was accredited to a heatwave during the previous summer ( Dipterists Forum, 2020). E. euchroma larvae have a mottled orange and white appearance which is species-specific within the genus ( Rotheray, 1993), they are aphid predators and have notably been found in the locality of fruit trees ( Ball & Morris, 2000). Adults are attracted to sunny spots of vegetation with a documented preference for the leaves of Acer pseudoplatanus (Sycamore) and Aesculus hippocastanum (European horse-chestnut) trees. It has been hypothesised that the elusiveness of this species could relate to it favouring residence high in the treetops out of sight ( Ball & Morris, 2015).
The genome of Epistrophella euchroma 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. The generation of a reference genome for Epistrophella euchroma will provide a valuable tool to further the understanding of this largely understudied species.
Genome sequence report
The genome was sequenced from one male Epistrophella euchroma ( Figure 1) collected from Wytham Woods (51.76, –1.33). A total of 42-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 19 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the assembly length by 1.26% and the scaffold number by 53.33%.
Photograph of the Epistrophella euchroma (idEpiEuco1) specimen used for genome sequencing.
The final assembly has a total length of 523.3 Mb in 6 sequence scaffolds with a scaffold N50 of 160.7 Mb ( Table 1). Most (99.99%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds, representing 4 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). 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.
Table 1.: Genome data for Epistrophella euchroma, idEpiEuco1.1.
Genome assembly of Epistrophella euchroma, idEpiEuco1.1: 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 523,327,223 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 (160,760,047 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (160,672,062 and 66,029,725 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/Epistrophella%20euchroma/dataset/idEpiEuco1_1/snail.
Genome assembly of Epistrophella euchroma, idEpiEuco1.1: 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/Epistrophella%20euchroma/dataset/idEpiEuco1_1/blob.
Genome assembly of Epistrophella euchroma, idEpiEuco1.1: 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/Epistrophella%20euchroma/dataset/idEpiEuco1_1/cumulative.
Genome assembly of Epistrophella euchroma, idEpiEuco1.1: Hi-C contact map of the idEpiEuco1.1 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=SZx4BiUcSxmDdVWIG6ziSg.
Table 2.: Chromosomal pseudomolecules in the genome assembly of Epistrophella euchroma, idEpiEuco1.
The estimated Quality Value (QV) of the final assembly is 63.2 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 96.5% (single = 95.9%, duplicated = 0.6%), 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/414814.
Methods
Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing was a male Epistrophella euchroma (specimen ID Ox001517, idEpiEuco1), which was netted in Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude –1.33) on 2021-05-31. Steven Falk (independent researcher) collected and identified the specimen, which was then snap-frozen on dry ice.
The sample was prepared for DNA extraction at the Tree of Life Laboratory, Wellcome Sanger Institute (WSI). The idEpiEuco1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer’s instructions.
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 tissue of idEpiEuco1 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 ( 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.
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.
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.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
- 1Abdennur N Mirny LA : Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz 540 31290943 PMC 8205516 · doi ↗ · pubmed ↗
- 2Allio R Schomaker-Bastos A Romiguier J : Mito Finder: 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 32243090 PMC 7497042 · doi ↗ · pubmed ↗
- 3Ball S Morris R : Britain’s Hoverflies: A Field Guide-Revised and Updated Second Edition (Vol. 17).Princeton: Princeton University Press,2015;17 Reference Source
- 4Ball SG Morris RKA : Provisional atlas of British hoverflies (Diptera, Syrphidae).Huntingdon: Biological Records Centre, Centre for Ecology and Hydrology,2000. Reference Source
- 5Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–319. 10.1016/j.ympev.2012.08.023 22982435 · doi ↗ · pubmed ↗
- 6Challis R Richards E Rajan J : Blob Tool Kit - Interactive Quality Assessment of Genome Assemblies. G 3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g 3.119.400908 32071071 PMC 7144090 · doi ↗ · pubmed ↗
- 7Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s 41592-020-01056-5 33526886 PMC 7961889 · doi ↗ · pubmed ↗
- 8Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. 10.1038/nbt.3820 28398311 · doi ↗ · pubmed ↗