Abstract
We present a genome assembly from an individual female Chalcis sispes (chalcid wasp; Arthropoda; Insecta; Hymenoptera; Chalcididae). The genome sequence is 412.4 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.9 kilobases in length.
Keywords: Chalcis sispes, chalcid wasp, genome sequence, chromosomal, Hymenoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Proctotrupomorpha; Chalcidoidea; Chalcididae; Chalcidinae; Chalcis; Chalcis sispes Linnaeus, 1761 (NCBI:txid1118640).
Background
Chalcis sispes is an extraordinary-looking parasitoid wasp. The family Chalcididae are instantly recognisable, at least in the British fauna, by their hugely expanded hind femora with ventral teeth and their curved hind tibiae. In the north temperate zone there are few species of Chalcididae and in Britain only ten species are known ( Dale-Skey et al., 2016). Ferrière & Kerrich (1958) provide a key to the British species which is mostly still relevant. The metasoma of Chalcis has a long petiole, and the hind coxa is also very long. Chalcis sispes is the most widespread of the three British species and like other Chalcis species inhabits the edges of water where its host stratiomyid flies can be found. Eggs of Stratiomys flies are laid in masses on emergent vegetation and C. sispes oviposits into the eggs, completing development in the larva when it emerges from the water to pupate ( Burks, 1979).
The family Chalcididae is morphologically and biologically diverse, especially in the tropics, and the huge hind legs, which have also evolved in a variety of other chalcidoids, probably fulfil a variety of functions. At least in Chalcis, the legs are used as robust props while manipulating the egg hosts with its fore and mid legs. They are also used in fighting, as females sometimes defend host egg masses against other females ( Cowan, 1979). The eggs of C. sispes are rather distinctive, with stalks at either pole ( Henneguy, 1891).
This first complete genome for the family Chalcididae will help unravel the evolutionary innovations which have enabled the extraordinary diversification of the Chalcidoidea ( Cruaud et al., 2024).
Genome sequence report
The genome was sequenced from a female Chalcis sispes ( Figure 1) collected from Parsonage Moor, Abingdon, England (51.69, –1.33). A total of 57-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 53 missing joins or mis-joins and removed 6 haplotypic duplications, reducing the scaffold number by 61.11%, and increasing the scaffold N50 by 4.70%.
Figure 1. Photographs of the Chalcis sispes specimen (NHMUK014036778, iyChaSisp2) used for genome sequencing.
The final assembly has a total length of 412.4 Mb in 13 sequence scaffolds with a scaffold N50 of 75.8 Mb ( Table 1). The snail plot 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 (99.96%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds. 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.
Figure 2. Genome assembly of Chalcis sispes, iyChaSisp2.1: 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 412,410,240 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 (85,135,257 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (75,805,882 and 69,969,611 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 hymenoptera_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CATLJJ01/dataset/CATLJJ01/snail.
Figure 3. Genome assembly of Chalcis sispes, iyChaSisp2.1: 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/CATLJJ01/dataset/CATLJJ01/blob.
Figure 4. Genome assembly of Chalcis sispes, iyChaSisp2.1: 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/CATLJJ01/dataset/CATLJJ01/cumulative.
Figure 5. Genome assembly of Chalcis sispes, iyChaSisp2.1: Hi-C contact map of the iyChaSisp2.1 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=dbWjnZj_RYOT9mV81R5qaQ.
Table 1. Genome data for Chalcis sispes, iyChaSisp2.1.
| Project accession data | |||
|---|---|---|---|
| Assembly identifier | iyChaSisp2.1 | ||
| Species | Chalcis sispes | ||
| Specimen | iyChaSisp2 | ||
| NCBI taxonomy ID | 1118640 | ||
| BioProject | PRJEB59203 | ||
| BioSample ID | SAMEA11025062 | ||
| Specimen information | |||
| Technology | ToLID |
BioSample
accession |
Organism part |
| PacBio long read sequencing | iyChaSisp2 | SAMEA11025310 | Whole organism |
| Hi-C sequencing | iyChaSisp1 | SAMEA11025285 | Whole organism |
| Sequencing information | |||
| Platform | Run accession | Read count | Base count (Gb) |
| Hi-C Illumina NovaSeq 6000 | ERR10818308 | 7.06e+08 | 106.56 |
| PacBio Sequel IIe | ERR10809405 | 2.21e+06 | 24.15 |
| Assembly metrics * | Benchmark | ||
| Consensus quality (QV) | 59.9 | ≥ 50 | |
| k-mer completeness | 100.0% | ≥ 95% | |
| BUSCO ** | C:93.7%[S:93.2%,D:0.4%],
F:1.3%,M:5.0%,n:5,991 |
C ≥ 95% | |
| Percentage of assembly mapped to
chromosomes |
99.96% | ≥ 95% | |
| Sex chromosomes | None | localised homologous pairs | |
| Organelles | Mitochondrial genome: 15.9 kb | complete single alleles | |
| Genome assembly | |||
| Assembly accession | GCA_949987625.1 | ||
| Accession of alternate haplotype | GCA_950005085.1 | ||
| Span (Mb) | 412.4 | ||
| Number of contigs | 457 | ||
| Contig N50 length (Mb) | 2.0 | ||
| Number of scaffolds | 13 | ||
| Scaffold N50 length (Mb) | 75.8 | ||
| Longest scaffold (Mb) | 85.14 | ||
* 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 hymenoptera_odb10 BUSCO set using version 5.3.2. 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/CATLJJ01/dataset/CATLJJ01/busco.
Table 2. Chromosomal pseudomolecules in the genome assembly of Chalcis sispes, iyChaSisp2.
| INSDC
accession |
Chromosome | Length
(Mb) |
GC% |
|---|---|---|---|
| OX465094.1 | 1 | 85.14 | 34.0 |
| OX465095.1 | 2 | 79.82 | 34.0 |
| OX465096.1 | 3 | 75.81 | 34.0 |
| OX465097.1 | 4 | 73.21 | 34.0 |
| OX465098.1 | 5 | 69.97 | 34.0 |
| OX465099.1 | 6 | 28.33 | 33.5 |
| OX465100.1 | MT | 0.02 | 13.5 |
The estimated Quality Value (QV) of the final assembly is 59.9 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 93.7% (single = 93.2%, duplicated = 0.4%), using the hymenoptera_odb10 reference set ( n = 5,991).
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/1118640.
Methods
Sample acquisition and nucleic acid extraction
The Chalcis sispes specimens used for genome sequencing (specimen ID NHMUK014036778, ToLID iyChaSisp2) and Hi-C sequencing (specimen ID NHMUK014036779, ToLID iyChaSisp1) were collected from Parsonage Moor, Abingdon, England, UK (latitude 51.69, longitude –1.33) on 2021-06-19 using an aerial net. The specimens were collected by Olga Sivell (Natural History Museum) and Ryan Mitchell (independent researcher) and identified by Ryan Mitchell and Judy Webb (Natural History Museum), and then preserved in liquid nitrogen.
The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the iyChaSisp2 sample was weighed and dissected on dry ice ( Jay et al., 2023). Whole organism tissue was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol ( Oatley et al., 2023). HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. 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.
Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io ( Denton et al., 2023b).
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 instrument. Hi-C data were also generated from whole organism tissue of iyChaSisp1 using the Arima v2 kit. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp 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 using the gEVAL system ( Chow et al., 2016) as described previously ( Howe et al., 2021). Manual curation was performed using gEVAL, HiGlass ( Kerpedjiev et al., 2018) and PretextView ( 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 | 4.1.7 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| gEVAL | N/A | https://geval.org.uk/ |
| 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/sanger-tol/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 | 1.1a.2 | https://github.com/c-zhou/yahs |
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, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>].
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]
Data availability
European Nucleotide Archive: Chalcis sispes. Accession number PRJEB59203; https://identifiers.org/ena.embl/PRJEB59203 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Chalcis sispes 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. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. 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.7139035.
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 Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.
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.
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