The genome sequence of the bulrush Neoascia, Neoascia interrupta (Meigen, 1822)
Steven Falk, Katie J. Woodcock, Iván Ballester-Torres, Luis Diambra
TL;DR
This paper presents the genome sequence of the bulrush Neoascia, a type of fly, including its chromosomal structure and gene annotations.
Contribution
The paper provides a high-quality genome assembly and gene annotation for the bulrush Neoascia.
Findings
The genome assembly spans 601.9 megabases and is scaffolded into 4 chromosomal pseudomolecules.
The mitochondrial genome is 17.76 kilobases long.
Ensembl identified 22,086 protein-coding genes in the assembly.
Abstract
We present a genome assembly from an individual female Neoascia interrupta (the bulrush Neoascia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 601.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.76 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,086 protein coding genes.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Figure 1
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Figure 4
Figure 5| Project accession data | ||
|---|---|---|
| Assembly identifier | idNeoInte1.1 | |
| Species |
| |
| Specimen | idNeoInte1 | |
| NCBI taxonomy ID | 2867103 | |
| BioProject | PRJEB55984 | |
| BioSample ID | SAMEA10166789 | |
| Isolate information | idNeoInte1, whole organism (DNA sequencing and
| |
| Assembly metrics
|
| |
| Consensus quality (QV) | 63.2 |
|
|
| 100% |
|
| BUSCO
| C:96.9%[S:96.0%,D:0.9%],
|
|
| Percentage of assembly
| 99.17% |
|
| Sex chromosomes | X chromosome |
|
| Organelles | Mitochondrial genome
|
|
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR10224919 | |
| Hi-C Illumina | ERR10297812 | |
| Genome assembly | ||
| Assembly accession | GCA_947623515.1 | |
|
| GCA_947622765.1 | |
| Span (Mb) | 601.9 | |
| Number of contigs | 373 | |
| Contig N50 length (Mb) | 4.0 | |
| Number of scaffolds | 38 | |
| Scaffold N50 length (Mb) | 219.1 | |
| Longest scaffold (Mb) | 226.7 | |
| Genome annotation | ||
| Number of protein-coding genes | 22,086 | |
| Number of gene transcripts | 22,574 | |
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| 1 | 226.68 | 39.0 | |
| 2 | 219.06 | 39.0 | |
| 3 | 128.09 | 39.0 | |
| X | 22.7 | 39.0 | |
| MT | 0.02 | 17.5 |
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.1.7 |
|
| 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
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Genetic diversity and population structure · Spider Taxonomy and Behavior Studies
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; Eristalinae; Milesiini; Neoascia; Neoascia interrupta (Meigen, 1822)(NCBI:txid2867103).
Background
The bulrush Neoascia, Neoascia interrupta (Meigen, 1822), is a predominantly black and notably small species of hoverfly found in Northern and Central Europe and Western Siberia ( van Veen, 2014). In the UK N. interrupta are found between the months of April and September and peak in numbers during June ( Stubbs & Falk, 2002). After a relatively recent addition to the UK species list in 1981, records of N. interrupta are most frequent in the East of England though individuals have been documented across Southern England, Wales and into South Yorkshire ( Ball & Morris, 2000; Ball & Morris, 2015). Adults display a preference for vegetation surrounding ponds, marshes, ditches and canals which are often rich in bulrush reeds, hence their common name, the bulrush Neoascia ( Stubbs & Falk, 2002). The species has additionally been noted occupying semi-brackish ditches in coastal areas of Kent and Essex ( Stubbs & Falk, 2002). N. interrupta is distinguished from other Neoascia hoverflies by the presence of yellow spots on the edges of abdominal tergite 4, which are lacking in other members of the genus ( Stubbs & Falk, 2002; van Veen, 2014). Females have a club-shaped lower abdomen, contrastingly males are more streamlined in appearance, though both sexes are noted for their distinct wasp-like narrow waists ( Ball & Morris, 2015). Species specific records of breeding and larval development are limited, though larvae of the Neoascia genus have been found in wet manure, compost and decaying vegetation associated with the banks of ponds and ditches ( Ball & Morris, 2015; Rotheray, 1993). Adult N. interrupta are frequent flower visitors and can be spotted flying slowly among low-growing flowers such as forget-me-nots and fool’s watercress ( Stubbs & Falk, 2002; van Veen, 2014). The completed genome sequence for Neoascia interrupta as part of the Darwin Tree of Life Project provides the opportunity to further investigate this understudied hoverfly species.
Genome sequence report
The genome was sequenced from one female Neoascia interrupta ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.76, –1.34). A total of 45-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 134 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 60.61%, and increasing the scaffold N50 by 14.82%.
Photograph of the Neoascia interrupta (idNeoInte1) specimen used for genome sequencing.
The final assembly has a total length of 601.9 Mb in 38 sequence scaffolds with a scaffold N50 of 219.1 Mb ( Table 1). The snailplot 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 (99.17%) of the assembly sequence was assigned to 4 chromosomal-level scaffolds, representing 3 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( 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 Neoascia interrupta, idNeoInte1.1.
Genome assembly of Neoascia interrupta, idNeoInte1.1: 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 601,923,271 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 (226,676,804 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (219,059,534 and 128,085,943 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/Neoascia%20interrupta/dataset/CANQKQ01/snail.
Genome assembly of Neoascia interrupta, idNeoInte1.1: 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/Neoascia%20interrupta/dataset/CANQKQ01/blob.
Genome assembly of Neoascia interrupta, idNeoInte1.1: 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/Neoascia%20interrupta/dataset/CANQKQ01/cumulative.
Genome assembly of Neoascia interrupta, idNeoInte1.1: Hi-C contact map of the idNeoInte1.1 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=LMw6NIp_REaXbeYMTvjmaw.
Table 2.: Chromosomal pseudomolecules in the genome assembly of Neoascia interrupta, idNeoInte1.
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 96.9% (single = 96.0%, duplicated = 0.9%), using the diptera_odb10 reference set ( n = 3,285).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/2867103.
Genome annotation report
The Neoascia interrupta genome assembly (GCA_947623515.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Neoascia_interrupta_GCA_947623515.1/Info/Index). The resulting annotation includes 22,574 transcribed mRNAs from 22,086 protein-coding genes.
Methods
Sample acquisition and nucleic acid extraction
A female Neoascia interrupta (specimen ID Ox001311, ToLID idNeoInte1) was netted in Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.76, longitude –1.34) on 2021-04-23. The specimen was collected and identified by Steven Falk (University of Oxford) and preserved on dry ice.
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; HMW DNA fragmentation; and fragmented DNA clean-up. The sample was prepared for DNA extraction at the WSI Tree of Life laboratory: the dNeoInte1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing ( https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1). Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher pestle ( https://dx.doi.org/10.17504/protocols.io.5qpvo3r19v4o/v1). DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer’s instructions.
All protocols developed by the Tree of Life laboratory are publicly available on protocols.io ( https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v1).
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 idNeoInte1 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., 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.
Genome annotation
The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Neoascia interrupta assembly (GCA_947623515.1) 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.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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